My least favorite Unovian Pokemon have to be...
Patrat (Ratatta I can handle. These are just... WHY? Also Watchog)
Gothita and its family (Like Ralts, but they aren't even cute. SO MUCH EYES)
Durant (The Pokemon is awesome, but annoying in the wild. I'd use it on my teams, but by the time I can encounter them, my team overshadows their absolute terror and epicness).
Vullaby and its family (Freaky vulture things. Original, but I like Rufflet and its line better.)
The rest I'm fine with. I do have issues with Snivy in the games, but it's awesome in the anime. Keldeo also gives me issues (FOUR musket deers? There are only three musketeers, not four), but I haven't seen it yet, so...