I'm mostly familiar with Nintendo, Sega, Sony games on PSX and PS2. My opinions are strongest about games on Nintendo platforms.
1. Metroid Prime - aside from graphical fidelity for the time, I don't see anything special about this one, the gameplay was fairly awful IMO. I like the idea of scanning, but when 95% of it is junk or repetitive junk info, and the switching of the visor, it felt WAY more intrusive than good - plus the tanky controls stunk.
2. Eternal Darkness - again, good idea, REALLY poor implementation. The game felt years out of date by the time it came out, particularly in controls. It was also not anywhere near as scary as some PSX survival and horror games.
3. Madworld - This game got so much hype and praise, and for what? Repetitive button mashing? Everything about it was really boring. I paid money for this one based on the over-hype and over-praise! ARRRGH!
4. Mario Kart Double Dash - I don't think it's a terrible game, but it's bad as far as Mario Karts go due to poor balance and bad/unmemorable tracks; the Mario Kart DD tracks are consistently the worst remixed tracks on more current Mario Kart games. The fact that it has people who claim its the best is why I think it's terribly overrated.
5. Final Fantasy 9 - This is one of those games everyone was disappointed with when it came out, but it had this bunch of defenders who became so devoted to their bullshit that people today actually believed this one was a good Final Fantasy game. This was the first Final Fantasy game to make zero attempts at advancing the RPG genre; the story was very flat, and much more childish than FF6-8 and tactics. The character art was atrocious, more along the lines of Crystal Chronicles than mainline Final Fantasy. I wouldn't attribute this to being part of Square's new philosophy, but they DID definitely want change as they headed into full 3D - FF9 was not developed by the main FF dev team, it was originally intended to be a spinoff title, but they wanted the "X" for the first 3D FF game, so they made FF9 a mainline game. It is also why FF7 (1997), FF8 (1999), and FFX (2001) are all spaced by the regular interval of two years, and why FF9 (2000) is jammed in between 8 and X in an odd time slot. If it was regarded more like a spinoff, then I wouldn't say this is overrated, but as a mainline game it is basically the most conservative and backwards game in the mainline franchise.
6. Chrono Cross - Had a huge argument about this one on this site already; I don't want to return there right now ;P
7. Legend of Zelda Wind Waker, Twilight Princess, and Skyward Sword - my biggest issue with all of these games is that, despite being significantly smaller than Breath of the Wild, and more linearly directed; they ended up feeling FAR slower and more sparse. The dungeons were oversized in all of them, and they were FULL of these "Get 47 of these random pieces of things, they're scattered over a gigantic area, and you need ALL of them to [progress to the next part of the game" or "pass this really obscure puzzle thing over this gigantic empty area" type stuff. I also found them to be too derivative of Ocarina of Time, and also much slower. They did add some interesting elements, each of them, but they were spoiled by the derivative framework and terrible pacing. Link to the Past, Ocarina of Time, Breath of the Wild were all great games; these other three (WW, TP, SS) should not be regarded as in the same class.
8. Gran Turismo - I know this shouldn't be here, because very few people are actually fans of this; in fact, it's the game that, to this day, is still common to see unopened in people's PSX game collections; not due to preservation, but due to disinterest in the game that came bundled with their console or replacement console. BUT, I recall a long time ago I was on this forum with two people who were gigantic fanatics of this game; and if this game franchise has ANY fans like that still alive, it is overrated.
9. Bravely Default - This is one of those games that starts off fine, it seems like it is going to get better; but then the part of the game where it is SUPPOSED to hit its greatness, is a repetitive piece of trash stretch; the game literally repeats itself over and over again - like you have to play New Game + multiple times to get to the end. People defend it by saying "but the first half is great!" - but NO, it's NOT, it's good, but never great. A game like Final Fantasy 7 or Chrono Trigger have great first halves; imagine a game like Xenoblade Chronicles 2 where they cut off the last 4 chapters and instead had you replay chapters 1-6 a few times before seeing the end of the game - chapters 1-6 of Xenoblade Chronicles 2 are significantly better than the first part of Bravely Default, but even then you would consider it a shitty experience if the game only had chapters 1-6. That's Bravely Default, it's a bad grindy GRINDY and repetitive game.
10. Knights of the Old Republic - This game was shit; it felt VERY unfinished with the shoddy cutscenes, character animations, and most of the art looked like it was stand-in. The gameplay is about the most uninspired I have ever seen in an RPG, and the battles look so clumsy that I am not sure how this made it to store shelves. It seems ludicrous that people actually think this one is good at all. If I didn't know better, I would have thought I got my hands on some kind of Alpha demo for what they wanted the actual game to be. There was nothing great about the story either, it was both flat and dry; and no, having hundreds of multiple choice questions does NOT make a story interesting - especially when everything feels so shoved in there for no other purpose than to have a bunch of multiple choice questions.
Of recent games: Super Mario Odyssey - I hate to put it here, because the game is an A+ title, just not the S+++ tier game that Breath of the Wild is and people are making THAT claim. First of all, it doesn't expand the franchise in a meaningful way like 64 or the Galaxy games did; it adds the cappy thing, which is cool, but we've seen those sorts of mechanics in Space Station Silicon Valley before, and Kirby to a lesser extent. The shops too; and the 2D platforming - but these aren't all that groundbreaking since Galaxy 2 had a significant amount of the 2D platforming angles as well - just not switching to 8-bit graphics. I found Odyssey lost more than it added to the franchise; and something about it, whether it be the challenge or the game length, felt unsatisfying. I don't think it's a bad game, but I did come into it immediately after replaying Galaxy 1 and 2 - and so I am comparing it to those. The argument I hear is that "it's the first non-linear Mario game since Mario 64!" and stuff like that... so it's interesting how it comes off feeling significantly more linear than the Galaxy games; sure the option is there to get the moons out of order, but that is not optimal or efficient, so it's ultimately pointless; ultimately, the Galaxy games feel more sprawling and more about picking the order of doing things; and FAR FAR more rewarding.
ON PC - I'd say the Master of Orion franchise, and Sid Meier's Civilization 4 - Civ 4 is a slower and less exciting game than Civ 2 or Civ 5; it's not as bad as 3, but 3 isn't as highly regarded. Some point to the different features that launched with it, but why would you even bother with Civ 4 in that case? Those features, like religion, are ultimately just really simplified version of Paradox Grand Strategy game features, and games like EU4, Vic2, and Crusader Kings 2 are SOOOOOO much better than Civ when it comes to the massive amount of features. Master of Orion because I found the entire game was always building up for one big push where you'll either win everything or lose everything.
These are games that I spent time with; I am not going into the various clone FPSs and Sport titles