You made me very curious, which one of the protagonists is it that you think doesn't suck? 

Arkham City.
Really good game. But I think the trilogy and even Arkham Origins thrown in are all pretty equal in quality. Origins played well like City and I liked the story still quite a bit too. Knight is my favorite Arkham game as I enjoyed the Batmobile, exploration, story, etc.

That's a tough one. People have mentioned Final Fantasy VII, and I think I might agree, solely because I've started the game several times but have never got more than maybe a few hours in, because the first few hours are really boring. It doesn't help that the game has really ugly character design and looks otherwise dated too.

Metal Gear Solid 3 is also a good pick here. It's a great game, but for a Kojima game, the story lacks depth, the bosses lack personality, and linearity really hurts a game that's set in a jungle - especially since the previous game in the series was way less linear, for the most part at least. I can see why people like it, but its flaws also prevent me from considering it as highly as some other games in the series.

Breath of the Wild
I have grown to detest the "open world" type of games because of it. It is fantastic that so many new people started to play the series because of it. But I long for another game using the old formula. I want to feel the urge. Like collecting chickens is a detour I almost feel bad spending time with rather than just another of the interchangeable make your own adventure objectives. The game I spent the most time in without finishing it. The success pretty much secured the future of the series being one I won't join.  

Diablo 2
When it comes to Diablo. For me nothing beats the original. When I play that game I actually feel afraid and the design of going further and further down till you reach the very burnings of hell is un matched for me in the series. Diablo 2 expanded sideways instead. And I get it, but I did not like it as much. The despair and almost hopeless aura of impending doom is not there. And what totally breaks the games feel for me is the respawning of enemies, something pretty much every action rpg does, and I hate it. Units, bosses and even levels respawning gives the player grinding abilities, but for me it takes away any meaning behind the act. Killing units does not matter since they are still there if you leave and return. 

I even prefer Diablo 3. They took a different route, emphasizing the run through same levels over and over. A completely different experience. Less systematic and more running through as much as possible. And it works for what it is. While Diablo 2 is somewhere in between, for me not excelling in either. Diablo 4 is the worst of the main line by a large margin. Maxing the things I dislike and removing the more childish aspects in Diablo 3. 

Michael. He isn’t great, he is a total prick, but at least he is a prick with a somewhat interesting character arc.

Crash 3. While I do think it's the most polished of the original trilogy, difficulty takes a step down from the second game, and I also feel too many of the levels are now side activities (don't know how else to phrase it) with the number of Jet Ski, Motorbike, Plane, Underwater etc levels. Pretty much only the Platinum relics are a challenge, almost everything else is a piece of cake.

Basically only 14 of the 30 levels are platform levels, (I'm not counting the two secret entrances to previous levels as separate.)

Though don't get me wrong it's still a wonderful game that I finished again just a couple of weeks ago. But Crash 2 is the pinnacle of the series to me not 3.

Monkey Island 2. I clearly prefer 1&3, the humor just doesn't work for me in 2, it feels stretched and these versions of Guybrush and Elaine are obnoxious.

Pleasantly surprised to hear that. I also liked Michael by far the best, but I've always felt like this was an unpopular opinion. 

I'll just list my most controversial ones 😄
Granted, these are just personal opinions, I'm not intending to say anyone else is wrong for liking different games from me. I see games as art, and so even the flawed/buggy ones are worth consideration over some more modern and polished games. So I don't really believe in good/bad so much as "I like this" and "I dislike this".

This is my format:
(Game often considered peak) → (Game I think considered peak)
(additional information)

Final Fantasy 9 → Final Fantasy 6

I think this is my least controversial opinion. Final Fantasy has a very diverse set of fans, and while FF9 wins the polls, it's still a minority of the fanbase usually somewhere around 22-28% - perhaps as high as 37-38%. I also think that generally more people would put FF6 ahead of FF9 overall. I actually have more of a top tier, it's FF6, Tactics, 8, and FFX, with my tier 2 being FF4 and FF7. But I think FF6 is the most beloved of those three... Really, I'm more an even numbered FF fan, as for the NES ones I enjoy FF2 the best as of the Pixel Remaster releases. Once we get above FFX, I'm less familiar with the series.

I generally enjoy the FF games that are more inventive and organically-story driven (This→but that→so this→therefore that) rather than the ones that are overly structured and sequentially-scenario driven (this→now this→now this→now this→now this...) and rely on just doing what was previously done with more polish. I don't find FF9 really stands out in any way, and I've never been too much of a fan of "sequence of scenario" type stories (which characterizes the early FF games) nor am I a fan of characters whose flaws are really more incidental than some kind of emotional trauma... To give an example: I often hear "Vivi is so great! The best character ever!" but his short lifespan isn't a character flaw, it's incidental, more of a wound. Think back to the story Vivi is based on, Blade Runner's replicants... the replicants share the same wound, they can only live in spans of 4 years... but that's not their flaw, their flaws were that they became psychopathic murderers, driven by their desperate attempt to extend their lives, and then vengeful when they failed... Vivi, much like the replicants, is an artificial being with a limited lifespan, and he was more like 'ho-hum, this sucks, but I'll move on"... in other words, just a character you feel emotionally manipulated to feel sorry for (much like the girl from FF5 whose grandfather died), it might manipulate your emotions, but it's not a compelling story.

I understand having a love for these sorts of characters one might like purely for the emotional attachment. There are some similar characters I liked from my childhood, but FF9 probably came a bit too late for me to appreciate that kind of character (It's kind of like Pokemon in terms of games, had I been younger, I'd probably have more attachment to the game). But I realize, in structure at least, the FF creators were trying to pay homage to the earlier FF games because it was the last numbered game... particularly FF1, 2, 3, and 5. These games, like FF9, don't have characters with flaws, it's just about building up strengths. Final Fantasy 4, while not one of my favourites, might be the most important game in the franchise for me. It's with FF4 that storytelling transformed into more flaw-driven story, characters lying, deceiving each other, dishonest to themselves... FF4 was also far more causal in its story, and this picked up with FF6. It was really the FF4 vein of FF games that I fell in love with, not the earlier ones.

Ocarina of Time → Breath of the Wild (and Link to the Past)

Ocarina of Time seems to still somehow beat out Breath of the Wild on lists. But it's at least close. And Link to the Past, while much declined today, was (pre-BotW) almost tied with Ocarina of Time as the most popular Zelda. Ocarina of Time would top all-time best game polls, but Link to the Past would at least make the top 10, often the top 5. I think it was the derivative Zelda games that really drove my opinion of Ocarina of Time down more, because I was more and more annoyed by some of the things that began in Ocarina of Time.

So, Ocarina of Time was one of the most massive releases of all time when it came out. The first Super Mario Bros game was already kind of in existence when it became popular. Super Mario Bros 3 was the first game I recall, in my life, with such a massive amount of hype. And it wasn't until Donkey Kong Country that I recall that type of hype happening again, and Ocarina of Time was next... although it took years to release.

I think part of it with this game was the pacing, the "dungeon" stuff... You see, I was looking for a game where I could stand atop death mountain and look over all of Hyrule. And at some point there were some ridiculous promises (not sure if it was early concepts, mistranslations, or fan craziness), but supposedly the world was big enough that it would take over a day to explore the whole thing. So... you can imagine my disappointment when it was really just a few small areas attached to one big open field you could explore in full within 5 minutes. The game had a lot of great little pieces to it, but it fell massively short of my expectation (unlike SMB3 and DKC).

Another issue I had was I was constantly annoying by the "find the next thing" progression. Everything was a fetch quest, a key, or a switch. The game was not very much about exploration so much as finding stuff in places you've familiarized yourself with. It lost that sort of "constantly going to new places and exploring them" drive that the original Zelda games had. It was, walking through the same caverns in the Water, Fire, and Shadow Temple I'd already been over 18 times. And these temples were also painfully long, I like being outside! 😄

Breath of the Wild was mostly outside, most of the wandering and retracing steps stuff was relegated to just four or five areas... which while important for getting major skills, ultimately optional. At the same time, that's about 8-10% of the game, instead of the 85-90% of Ocarina of Time. Finding a key isn't a problem in 2D, but I think it didn't translate well into 3D, and I'm glad Breath of the Wild minimized it. Breath of the Wild, apart from fixing or greatly reducing all of the problems of Ocarina of Time I had, also gave me that experience I so craved as a teenager: looking over Hyrule from atop Mount Doom.

But it also gave me this moment, right at the beginning... now one of the most famous shots in video gaming history:

The game definitely has its positives, but the overall experience wasn't for me.

Sid Meier's Civilization 4 → Sid Meier's Civilization 2

This one probably draws less opinions on this forum, but former King Civ 2 is a distant second behind 4 today, and for many years now... although, Civ 5 may be ahead of it too, now. So this is my second most controversial opinion.

This has to do with Civ 2 being a proper 4X game, and Civ 4 not being such. There was a time when Civ 2 was basically King of PC gaming, and very much king of strategy gaming. But at some point Civ 4 usurped it as the most popular Civ game on the Internet.

In short, what does 4X Mean? It stands for
eXplore
eXpand
eXterminate
eXPloit

The exploration, was something that went until the age of exploration... really until satellites, but Civ 4, all the exploration is pretty much in the first 5% of the game or so. There was more to explore, but it was really more for interest, as there was no real value to it unless you were expanding your religion to other cities... usually you exchange maps and discover the entire world that way. So, that's one X down for Civ 4 that Civ 2 does well.

Civ 2, you could expand relentlessly, colonization was a big part of this game. But Civ 4 had extreme penalties for playing wide (building lots of cities), and encouraged players to play in just one way, tall... that was far more efficient and a much stronger strategy. But both tall and wide strategies were valid in Civ 2. So that's 2X for Civ 2, 0X for Civ 4.

Civ 2, warfare was a big part of it, you would often fight a series of wars against other expansive civilizations, but you'd end it because of war weariness, or accomplishing your goals. Or maybe, just warring for an eternity against the bloodthirsty tyrant Mohandas Gandhi. Civ 2 was very war heavy.  In Civ 4, if you expanded through military conquest, prepare to be the most hated civilization for the rest of history... you won't recover. Best to stay peaceful in Civ 4, that's the name of the game. That's 0X for Civ 4, 3X for Civ 2.

Exploitation was the name of the game for Civ 4. It's really just a 1X game. Think SimCity type game, you carve out a small part of the world, exploit the resources, exploit the trade, exploit your religion, and just take in as much wealth as you can, build→exploit→build→exploit. Civ 2 doesn't do exploitation as well, so if you're a big fan of that X and not the other 3Xs, you'll probably prefer Civ 4, but if you want a great 4X experience, Civ 2 is the best one of the series... it wasn't until Stellaris that I had as much fun with a 4X game again.

Also, Civ 2 had these guys:

And the live action Wonder videos, that IMO haven't been topped:

Metroid Prime → Metroid (NES)

This is my most controversial. I know Prime is by far the most popular game in the franchise, followed by Super Metroid. I expect very few (if any) to agree with me here.

Now this one, I fully admit, has a lot to do with nostalgia bias. Some of the things Metroid does are things that drive other people absolutely crazy.

First, to get the Metroid Prime stuff out of the way, a lot of my criticisms are much like Ocarina of Time "find the thing somewhere to move forward". But on top of that, I wasn't a fan of the lenses thing, scanning all these things is interesting, but I hated how things were gated behind it, particularly because a lot of the scannable stuff was redundant, or kind of nonsense. So, it felt like a bit of forced intrusion on the experience of running through the world and shooting stuff. Another thing is first person games tend not to grasp me as much as third person. It's not a universal thing, I really like high-action FPS views, but not so much this. A lot of the time I got Myst vibes. That works very well for a lot of people. Not so much for me.

With the original Metroid, the game was quite open world. So while there was a lot of finding, it was more exploring and finding, like Breath of the Wild, rather than searching through the same spot to find what you need to progress. Metroid gave you almost the entire world right after the tutorial section. So yeah, you want a good predecessor to Breath of the Wild? Metroid! The first section of Metroid is like the Plateau, you learn the game basics to clear it, then the world mostly opens up as soon as you clear it. All created by Yokoi and Okada → who (in another post) I identified as two of Nintendo's Mount Rushmore along with Miyamoto and Tezuka for creating the philosophies and game design principles that guide Nintendo. The music of Metroid was also phenomenal, one of the first soundtracks that really grasped the themes of a game... at least that I came across.

The part of Metroid that drives most reasonable people insane, but I love, is the severity of punishment for screwing up. So, it kinda flips the whole old-school RPG mechanic on its head of "grind to progress your character so you won't fail the next challenge" into "fail the next challenge and you'll have to grind before you can try it again!" Because, if you screw up in Metroid, it'll be 5 to 45 minutes of grinding depending on how far you are in the game... (toward the beginning, it's relatively quick, but at the end it can take 45 minutes to fill your power). Nothing gives me more terror than the prospect of having to grind... in a way, that part of the game adds to the dread of Metroid, along with the music, the colours, and the general atmosphere of having the aliens everywhere. But Metroid's world also has some kind of majesty to it that has never been replicated... I will admit, the outer world in Metroid Prime 1 managed it, but that's about all I can recall of it.

I played Civ 1 so much back in the day that when I did get Civ 2, I didn't have much interest to it (nor ever since).
Decades later (just couple years ago) I finally returned to Civ with 4 and I did enjoy that like the first almost thirty years earlier.

FF6 is my favorite of the series. But I also like 9 better than 7 or 8.