Final Fantasy X is the epitome of this for me. I don't hate the game, but I enjoy it.. for all the wrong reasons. It's both one of my favourite games, but also one of my most hated.
1: The character design, Tidus and Lulu in particular. The former wears shorts with different-length pant legs and a midriff-baring wife-beater thing with a hoodie over it. The latter wears a dress made of belts.. That's not even getting into the fact that Wakka's hair is stupid as all hell, maybe even the worst, and that Tidus looks like Meg Ryan.
2: Yuna is not the protagonist. This is an issue in and of itself. Fuck Tidus. I do not care about Tidus. I do not care about his story and his little bitchy ass character development arc. Those 5 minutes in which you play as Yuna instead of Meg Ryan over there were the best 5 minutes in the game for me.
3: The Sphere Grid was a good idea, brought down horribly by the fact that it just doesn't work out all that well. It should have been secondary to main character development, and forcing the player to use a gimmicky, unreliable, confusing system to level up their characters was not fair or a good design decision. Whoever made it should be forced to drink gutter water for the rest of their life.
4: Happy fireworks. The laughing scene. Even if these moments, and many many more, were intentionally badly and poorly handled... that doesn't make it any less badly and poorly handled.. HAHAHA, HAHAHA, HAHAHAHAHA, HYAHYAHAHYAHYAHA, HYAHYAHAHAGFIEHGFEHGEBGBEGFB
5: Riku, in general, is just ridiculously disturbing. Really tasteful, Square, making the resident kid hero 15-year-old girl (and that's only by the end of the game!) the local fanservice girl. While not entirely related, the hot spring scene in X-2 cemented her as my least favourite female Final Fantasy character, simply due to the fact that she's walking loli-bait. Not cool.
Also, Dark Souls. This game.
1: With some colourful sequence-breaking, perhaps even by accident, you can turn this otherwise difficult, unforgiving game into a glorified catwalk. I've seen runs where by Blighttown, players have ridiculously powerful weapons and have used the Master Key to skip most of the bosses, making bosses like Spider-Booby Lady (now canon) powerless in your overleveled wake. A game should not be this broken, especially not from the very start.
2: The characters are boring. They mostly just exist to show the player how broken and desolate Lordran is, and that's... all they do. You find some of them in various locations having gone Hollow and are forced to kill them, but aside from that, they... don't do much. They sometimes do a thing, but not many things. Sometimes, they sell you stuff. But aside from that, eh? Do you honestly care?
3: Some bosses are sort of shitty. Some of mini-bosses (no, not the mini-mini-bosses) like the Taurus Demon and Hellkite Dragon sort of suck. For good fights, there are the Vagina Vomit of Death Dragon, the beloved Ceaseless Discharge, and the aforementioned Spider-Booby Lady, and Priscilla. Except I hate Priscilla because she will never become my waifu desu desu, so fuck Priscilla.
But aside from those big-game bosses, and a few others, the rest of the bosses are just shitty. The AI is disappointing, and outright doesn't work, in some cases, leading to many hilarious incidents of formidable bosses and intimidating NPCs alike doing things like backflipping off cliff faces and turning in circles forever.
4: The Upgrade System. A few paths don't seem to have been finished at all, the Raw path being the most glaring, and Magic or Divine over 5 are just useless. They're only worth it for unlocking Enchanted and Occult.
5: The controls stack, like the older Quest For Glory games. This means that you might roll or attack with a lunging weapon when you don't want to, and then get murdered by some fat asshole because the controls are awful.