I've noticed a trend I have over the past few years where I enjoy a game more when I played it than others, but then I end up forgetting it. For example I feel like Resident Evil 4 was the game I had the most fun playing, but not too long after I played I've sort of forgotten about it. However, I still feel nostalgic for the original tank style Resident Evil games and think about them pretty often and fondly. A similar thing happened with MGS1 compared to 2 and 3. MGS1 is the game I look back on the most, which is why I started The Twin Snakes yesterday.

Memory relies on our feelings at the time of creation and - because our brains are poorly designed - it remembers the less positive feelings better than the great ones. Basically, when we're disappointed but still enjoy a game, we'll remember it better because our brains remember negativity better.

I've noticed what you're saying too as very few of my favorite games are both incredible and fondly remembered(off the top of my head only Red Dead Redemption and Final Fantasy IX achieve both).

Probably doesn't address the point you're trying to make, as the games you've mentioned have plenty of memorable sequences and moments, but sometimes enjoyable games just don't have anything to "stay with you". I can't remember anything from Alan Wake outside "running through the woods with a flashlight" and "kickass concert scene" when it comes to gameplay aspects of it, and yet it was a very enjoyable game for me.

Also you probably keep trying to see sparks of brilliance in these enjoyable games akin to those you remember fondly in the other games, which might obscure the actual brilliance moment of those games themselves and thus making them not so memorable.

They definitely weren't negative experiences. It's just works in a way that my favourite experience playing through is different from my favourite game in hindsight.

Final Fantasy IX was a good game too.

There could be a number of different factors at play here, but one could be that when it comes to games that stay with you it's the characters and story that left the most impact, while in games that are the most enjoyable to play it's the gameplay that shines the most. So you might still remember it fondly in hindsight because of how much fun the game was to play in terms of gameplay, but can't recall many specific things about the game because the story or characters didn't leave as great an impact as some other games did.

Of course, it could be something completely different too, but that's one reason I could see for it at least.

That's probably it along with the music.

Most things that "stay with you" do so because they succeeded in crafting memorable moments. It doesn't really matter the form of media, standout moments can elevate the entire experience because that's what sticks in your mind. It's what you walk away with, so it's a major factor in forming that memory. Something that is uniformly good throughout might not have the same effect.

Personally, I think it's age related. Most of my memorable gaming moments is when I was in single digits. Like I can remember details for every game I played when I was an innocent child. Background design, soundtracks, levels, characters, etc. Nowadays my jaded-ass forgets the main character's name after a few hours.

Same for me, but I think it is a been there done that kind of thing. I remember all my Atari, NES, SNES, N64, and PS1 games down to the finest detail. Then it starts to get fuzzy with PS2, only a dozen titles I have deep memories of. Then with PS3 it is maybe a handful. On PS4, XBO, and Switch, I have enjoyed many expereinces, but I could only give you details on a few titles. With PSVR though. I can vividly remember every single game and expereince I have had. 

I think it comes down to impactful new expereince, that completely go beyond your expectations. For me that is uniform across games, information, events, people, and anything else. The first holy crap moment is etched to the very core of my fabric, after that each additional repeat or incrementally more impressive moment memory is just a footnote. 

The Uncharted series is a good example. In my memory, I absolutely adore Drake's Fortune, I love everything about it, I can pretty much remember every piece of Music, and every scence. Where as I remember enjoying playing Amoung Thieves, Drake's Deception, and A Thiefs End more, but I don't look back on them in the same light, nor do I remember half as much about them. Lost Legacy, however, I absolutely love, and remember vividly. So, initial great expereince, followed by incremental upgrades, and then a new formula. I remember the initial expereince and the new formula, but the inbetween is just a hazzy, but great time.

Hmmm. I really enjoyed Tales Of Symphonia on the Gamecube, but I don't remember it well. One theory for this was the incredibly large amount of battles that broke up the narrative. Yet, FF XIII ( yes, please feel free to s*** my b**** ), which had a similar number of battles, and a brutal plat grind, sticks with me way more. I often like to pull down my pants and dump on MS, but Halo still sticks with me big bigly. Loved at at the time, and my recall of it is very strong. But it's a different game, right? I played all those set pieces so many times.....I liked inFamous: Second Son more than Styx: Master Of Shadows, but Styx stuck with me more. I don't know if it's been addressed, but one's own life is also a factor. The intensity of positive and negative emotions surrounding a playthrough is going to play a role in how a strong a person's attachment is to a piece of entertainment. What was the game you were playing when your family was beheaded? When you did mushrooms for the first time after a concussion? When you first beheaded somebody? Events like these help to bolster/weaken attachment.