I seriously can't think of anything wrong with it. It is the definition of perfection.
OK fine... uhh the sequels aren't the greatest? Legit complaint I guess would be that it's a lot more linear than other Metroid games in terms of item progression. The way you sequence break in it is really by using programming glitches and not actual skill techniques like bomb jumping.
Xenoblade, the game has incredible music and atmosphere, and the battles are fun. My beef is with the somewhat cliched storyline, and also Riki being incredibly annoying and ruining the atmosphere of any important event by saying something Scrappy Doo-esque.
I also didn't like the designs of the different races. The High Entia just have derpy looking wings on their head, and the Nopon are uninspired balls of fluff, and the Machina look like dark elves (yeah, it makes sense plot wise, but it would have been cool if they had a more clockwork look to their design).
Oblivion, unplayable without overhaul mods. And yes I realize that's a bit silly to say my favorite game sucks vanilla, but it has all the tools it needs to be one of the best games in the series and ruins it ALL on the garbage level scaling and leveled loot.
I plan on building a mod for it that changes ONLY the leveled loot and enemies, because I hate the overhaul mods for packing the one feature I want with a bunch of other features I don't (like certain weapons that tank your FPS from 60 to 2 when you look at them.) --- Scientifically proven.