Majora's Mask:
As much as I love the game, the first four hours of the game (when you're stuck with Deku Link) almost turned me down the first time I played it, and is quite a problem when I want to recommend the game to someone. I'm aware why it was done, but so many people seem like they were turned down from this game by this part alone, which is really sad to hear since this is not just my favorite LoZ, but one of my favorite games of all time.
Castlevania: Symphony of the Night
Second half of the game is just the castle... only upside down. While that change did result in a few interesting rooms to travel through, some areas really didn't benefit from this. Ends up feeling like pure laziness from the developers. Also, the song is the same for most areas.
Danganronpa (the series)
Without spoiling anything, I love a lot of the characters in all three games, but there are some you know were just put there to fill space or to be killed. I think this is way more evident with Danganronpa 2.
Fire Emblem Echoes: SoV
I know this is a remake, but... couldn't some of these maps get remade or something? Especially the desert ones in Celica's side, seriously.
Speaking of Celica, she starts as a really interesting character, but Act 4 throws her under a bus. And in Act 5, it's up to Alm to save her... because she can't save herself on her own, apparently. She had so much potential to be a great female protagonist, but then this happens.
Also, the whole thing with the DLC is just pure BS?
Final Fantasy Tactics: WotL
REALLY hard to get into at first because the game doesn't explain its mechanics in the most ideal way. You can only learn anything about the Jobs mechanic for explain if you either mess around in the Jobs menu or read the utterly boring text tutorials the game offers. Better than nothing, but still not exactly what I'd call "good".
Really, and I mean, really easy to break.
After playing Fire Emblem, the fact this game has no way of skipping enemy actions or any sort of fast-foward button annoys me a bit.
I wrote way more than I actually wanted to, haha. Sorry 'bout that.