The first name that sprung to mind was Barthandelus or however you spell it from FFXIII. I can see the dislike for Ultimecia, too. Really, though, my biggest dislike has to go to any final boss that has barely featured throughout the story. I'm looking at you FFVIII/FFIX/FFX/FFXIII. I had very little to zero dislike for these bosses because they were just thrown at me near the end. I mean, I can see that they had long-standing input to overarching plots (well, some of them) but seriously, all of those games could have had notably more relevant final bosses.

I also can't stand Seymour for FFX. The guy's voice annoys me too much.

Outside of Final Fantasy, Marauder Shields of Mass Effect 3 was another example of a final boss being completely random. And for generally crappy bosses, I guess there are too many to name and the worst of them I have forgotten the names of altogether. They're that bad that I just don't even remember them. Uncharted's bosses are a good example of this. I'm not sure I can name a single one despite getting the platinum trophy on a couple of them. I think bosses in shooter games tend to be pretty meh.