My favorite Gen is of course, Gen V. Yeah, big shocker. Now, I'll do this if everyone's willing to be mature about it (that includes Mods and Admins). There's a reason I held off on talking about this for so long. Alright, here goes:
My least favorite thing about Gen V was Ghetsis. Make no mistake, I don't by ANY means think he's a bad JRPG villain. I just think he was miscast in a game that he really shouldn't have been in. If anything, he should have been in Gen III or Gen VI. He would have fit in a lot better in one of those two.
Here's why having him in Gen V was a bad move. In Gen V, you have a plotline about the ethics of Pokémon Training and Battling. Admittedly, the evil Team of the game is made up of a bunch of hypocrites that are willing to use their own Pokémon to battle for them, even though their ideals suggest they're against this. But putting that aside, the concept of a villainous group that legitimately thinks they're doing the right thing, makes them a much more interesting faction. It gives them a reason for their actions and makes them more than a simple strawman group that you just have to defeat to move forward.
Then in comes Ghetsis and says, 'Nope. I was just manipulating them all along to get a Legendary Pokémon to take over the world.'. No motivation. No ideals. Nothing interesting. And this happens at the last second in the game too. Now understand that I have nothing against a villain that has the simple motivation of wanting to take over the world. But in a game where they were addressing the subject of the ethics of Pokémon Battling and Training, it just feels so out of place.
And I will say that it's pretty obvious that editing came in and made the decision to use him as a way to give the plot a tawdry resolution (I can even tell exactly where editing came in on this). They never really address the original subject matter, outside of some self-righteous preaching by some of the characters that's pretty asinine if you think about it for more than two seconds. It is the one blemish on what would have otherwise been the best storyline we ever got in a Pokémon game.
Make no mistake. This is still one of the best games in the series. I mean come on. This is the game that literally has a trash Pokémon! That alone makes it amazing! I was finally able to have a Pokémon that I could name The Trashman!
My least favorite Gen is probably Gen VI, though I don't really consider any game in the series particularly terrible, and I really don't have a long list of things that made me hate it. On the contrary, it's just a point in time where I lost interest in the franchise for awhile.