Honestly Gen 3 was my least favorite overall, and had a lot of pokemon I dislike.
Nobody's said this yet, but I never cared for Poochyena, I'm not a dog person so I was never fond of this thing. Doesn't help that it's one of the first pokemon you see so it sets the stage for the rest of the game. (For the same reason I don't really like Elektrike, but Manectric is awesome.) Then you have Wingull/Pelipper which I also hate, not only because, as people have mentioned, you run into about 9,000 of them throughout the course of the game, but Wingull just looks sloppily designed and anatomically impossible. Like someone went to an arts and crafts store, spent $2.54 on cheap assorted paper and whatnot, glued it all together and it somehow came to life.
Another problem I have with pokemon often is that their final evolution often looks worse than their earlier forms, in this game that's completely true of Ludicolo. Like, Lotad is awesome, it's this derpy, squattly little thing that just stares at you awkwardly, who couldn't like that? But then Ludicolo looks like some kind of Mexican nightmare clown on PCP. Also, I think Lairon is one of the coolest looking pokemon of all, but Aggron is kinda meh. (I have the same problem with Rhydon and Rhyperior btw.) Slaking is also not cool compared to it's earlier forms. I think Whismur and Exploud are ok, but Loudred is stupid looking. (I guess I just hate pokemon with huge gaping mouths, except Golbat, Golbat is awesome.) Spoink to me is awesome, one of the cutest things ever, but Grumpig is a big fat ugly thing. Never cared for Baltoy or Claydol, like, how are things that resemble artifacts from an ancient culture that should be in a museum supposed to be pokemon? Huntail is derp city and possibly the ugliest pokemon ever. And call me crazy but I've never been a fan of Numel or Camerupt either. (Althought I suppose Camerupt is kinda cool design-wise.)
Then we have this games one off pokemon that don't evolve, and a lot of these are silly too. Volbeat and Illumise are just dumb. Same thing with Plusle and Minun, I mean they're cute, but not terribly useful, they're just annoying, and not different enough from each other for there to be two of them in both cases. Solrock and Lunatone are Kirby villains that shouldn't be pokemon. Nosepass is ridiculous (Probopass is more ridiculous but not in this game.) And I never have and almost assuredly never will use Castform.
I was gonna say Spinda, because honestly, that thing is useless and annoying, especially when you're running around collecting ash and have to fight millions of them. But at least in X&Y and ORAS Spinda stumbles around like it's drunk as hell and that makes me laugh every time so I'll give it a pass.