My only real beef with Gen V is brutal centralization it has put on weather teams. Particularly sandstorm teams.
I'll bet half the teams I'll fight will be some variation of Tyranitar/Hippowdon, Choice Scarf Landorus, Excadrill, Reuniclus, Ferrothorn, and Metagross. Honestly, weather teams depress me. I don't know why, they just do.
Sure, some of the new Pokes looked stupid or had bad names, more so than any preceding generation, in fact, but what did we expect? Most of the good ones have already been taken.
I actually liked the storyline more than any other game so far. Gen I barely had a storyline, Gen II was largely about fighting an already doomed Team Rocket, Gen III was WAY too centralized around the primary legendaries, Gen IV had the storyline JUST at that point where it felt like they were trying too hard without any real result. Gen V, however, while it does seem like they're still trying too hard, yielded great results, despite seeming stupid at earlier times in the game.
I liked the characters a good bit as well. Cheren, while not as good a rival as the original from Gen I, fits the rival niche pretty well. Also, him + Bianca, whom I admittedly dislike, mean 2x the rival battles without too much of a loss of the "Oh yay! Rival Battle! YES!!!!!" effect. The gym leaders were pretty cool, and I loved N, although he was overdone a bit.
I really want to say it was one of the best gens yet, but then I remember how great Gens I/II were, and so Gen V has to take the middle spot.