Gen 2 is my favorite, even though Johto has some serious flaws.
Gen 6 was a rushed mess. Excluding Gen 5, stories in Pokemon games are usually nothing to write home about. Gen 6 managed to one up the rest of the series by having the most awkwardly written story. It's so bad, I almost want to say it was intentional. Legendaries who have zero lore behind them or purpose. Team Flare, a group of vain and selfish people, has a guy who hates those exact kinds of people as a leader. Malva being a member of team flare. The team flare scientists serving no purpose. And my favorite. Lysandre wearing that awful mechanical getup in your last battle with him. I just had to start laughing at that point.
Sky battles were the worst thing introduced to Pokemon since Pokemon musicals. Because of sky battles, stuff like tropius and Xatu have terrible 3d models where they must forever float idly in the air. And if a flying type Pokemon doesn't have a model where it's doing this (farfetch'd, hawlucha, etc), then it can't even participate. For some odd reason, gamefreak pushed this battle type in game more than rotations, triples, or even doubles. Inverse battles too.
It's not all bad since looker's quest was well written. Pokemon Amie and the PSS should definitely remain series staples. And EV training / IV breeding have become more accessible than ever. But X and Y just felt incomplete. And when is gamefreak ever going to fix the GTS so that you can't ask for Pokemon that they don't allow you to trade?
I don't count remakes as part of a generation. Otherwise, fourth gen would have something going for it outside of platinum.