I'm only listing the really major ones.
i.e. I wouldn't mention Kirby Canvas Curse or Valkyrie Profile because, even though I do think they're overrated due to non-existent replay value in both cases, I did still have a lot of fun with them one time through.
Nor would I mention Final Fantasy Tactics Advance, Riviera, Metroid Prime 2, or Secret of Evremore, because those games get low enough general praise anyway that my own hangups with them aren't worth explaining.
Finally, games like Mario 64 or Wind Waker are also excluded because while they don't really blow me away, they're still enjoyable enough that I think it's safe to say that I "get" them.
Anyway...
-Paper Mario. (The original. I'll buy the sequel when it hits $20, but haven't played it yet.) The battles and the walking speed are both too slow-paced for me, especially when compared to the later Mario and Luigi games. I feel like the timed attack system actually works against the gameplay here.
-Halo and Halo 2. Aside from Turok and Duke Nukem, I haven't played an FPS that isn't at least this good. Unreal, Half-Life, Goldeneye, even Perfect Dark and I really didn't care for PD (wouldn't even pay $9.97 for it as the N64 was dying)... What in the world is all the hype about?
-Final Fantasy VII. Annoying load times before battle, irrelevant mini-games everywhere, possibly the worst-looking map screen character models ever, a contrived plot full of extraordinarily stereotyped characters, and a dull soundtrack that had one guy I knew of actually turning it off to play his FF6 CDs instead.
-Final Fantasy VIII. The Draw system has to be the most unbalanced and boring feature in any RPG I've played. And the GF/orphanage plot "twist"? Awful. Just awful.
-Grand Theft Auto series. What's the point? People complain about backtracking in some games, but this is the ultimate as far as absurd amounts of backtracking go, and nobody ever brings it up. Just because the world is huge doesn't somehow make it fun for me to move around. Shoot, I've been complaining about the size of worlds since Ocarina of Time, and that wasn't nearly the size of GTA games these days. Speaking of which...
-Legend of Zelda: Ocarina of Time. Were people just impressed because Hyrule Field was big and beautiful? They made the shield ubertastic, gave the enemies such absurdly easy-to-exploit patterns that they'd have been better off with the completely random movements of the NES game, and the item set was terrible compared to A Link to the Past--no Bug-Catching Net, Good Bee, Magic Cape, Bombos, Ether, Quake, Cane of Byrna, Cane of Somaria, Pegasus Boots...
-Suikoden 2. The battle system is too generic for me to be interested, despite the really cool soundtrack and huge cast of characters. I actually gave my copy of this to a friend and then regretted it, but only because I thought it was worthless and then saw two weeks later that I could have traded it in at Gamestop for $30 in credit.
-Realistic sports games in general. Why does anyone play them?
-MMORPGs. I played a text-based game for years when I was 11-13, and then I realized that it was just a massive waste of time where levelling took about ten times longer than it rightfully should. As far as I can tell, every other MMORPG is the same way. Why would I pay a monthly fee that eventually adds up to like $200 when I could have bought and fully completed 4-7 games for the same price and in the same amount of time?
-Tekken. The aerial game doesn't play nearly enough of a role. This may be a bias of mine just because it plays so much of a role in SSB that it's become my specialty, but in Tekken the fighters practically feel nailed to the ground. Unless I just never figured out how to do more air-based moves or something...
-Jak 2. I never played the original, but apparently it's better. Even cutting out the extremely boring hub world navigation (too much traffic in the air, too many soldiers on the ground, having only two hover zones is asinine, and most of the vehicles control like they're Wave Race jetskis or something), though, and trying to pretend platforming was the only aspect of this game, I don't see where the appeal is. Why has platforming sucked ever since it went 3D?
-2D Bomberman. One of the extremely rare cases where I think a franchise got better with the transition to 3D. I don't understand why people demanded a return to the boring plus-shaped explosions after the awesome fun to be had with the dome-shaped area explosions in Bomberman 64. For that matter, every Bomberman game should start you off with the bomb kicking and throwing abilities from the very beginning.
-WWE Smackdown series. People like this arcade-y garbage? I often can't stand realism, but nobody should be getting up five seconds after getting thrown off a HIAC, nor should all your moves be so terribly choreographed as they are. The special system is another reason I can't stand the series; moves like the toe kick become too obvious and too predictable.
-WWE Day of Reckoning series. If they want to emulate No Mercy, they should take the No Mercy engine and build upon it, not try to develop some kind of meeting point between NM and Smackdown. I want visual tapouts in a match with no submission victories. I want the Losing It system. I want KOs to look like KOs. I want Japanese moves, and lots of them. I don't want highly overpowered A-damage and S-damage moves as strong grapples. I don't want to be able to roll out of the way of a stomp four seconds after taking two Stunners. I want flying moves to actually connect sometimes against a halfway decent human opponent.