Gen 1 - Good: Well, they're fun to play, even if they're a bit dated.
Bad: Muk is my least favorite Pokemon ever. I don't care if it's useful, it's literally just a bigger Grimer. In fact, I'll just say the less creative designs in general are my least favorite part. Even I don't like Gen 6's lower Pokemon roster, but hey, quality over quantity, right?
Gen 2 - Good: Genders, the day and night system, the Pokegear, in-battle Pokemon animations... Oh wait, I can only list one thing? Oops, sorry.
Bad: Tough to think of, I'd say Whirlpool being an HM is the worst thing for me. Whirlpool's pretty useless as a move.
Gen 3 - Good: Pokemon XD and Colosseum did a pretty good job of doing something new with the series and I would totally support a sequel on the 3DS or Wii U. But then again, that will never happen.
Bad: The trade restrictions. Was it necessary to require you to beat the game to trade with other Gen 3 games?
Gen 4 - Good: HeartGold and SoulSilver. Now that is how you do a remake. Take what was good about the original, streamline it, and add some new features and content that either adds on to the existing content or doesn't intrude too terribly.
Bad: Saving a lot of data...
Gen 5 - Good: Their attempt at telling a deeper story went very well. It threw some unexpected curve balls and gave us some well-developed characters.
Bad: Did we really need an event to get Zorua and Zoroark in Black and White? It was better in Black 2 and White 2, but I was a little annoyed I couldn't nickname it.
Gen 6 - Good: OH MY GOD THEY STREAMLINED EVERYTHING PERFECTLY! EV Training isn't a pain to do, Wonder Trade's a fun way to complete the Pokedex or get rid of crappy catches, you can change abilities if you don't like them, gameplay-wise, these are the best Pokemon games to date.
Bad: X and Y was underwhelming in comparison to Black and White story- and character-wise. The rivals are all pretty flat, the evil team's admins are just kinda there and you never see them all in the same room, AZ popped up like three times and could've been elaborated on more, Lysandre could've been better-developed, and Diantha had no personality other than "I'm a celebrity, let's have a Pokemon battle sometime." I could go on, but in the end, I honestly still like X and Y, just... Play it for the gameplay, not the story.