I've played through Generations 1, 2, 5, and 6.
Of those, I think my favorite is Gen 2, because it expanded a lot on Gen 1's selection, and there was some really cool Pokemon there. It was basically Gen 1, but with more stuff, and it was back when the Pokemon games were actually purely about your Pokemon journey. The later games get too wrapped up in trying to make them big and epic that it distracts from your true goal. Forcing you to stop your journey and try to save the world from these huge, catastrophic events involving villain teams and legendary Pokemons, when that's not what I feel Pokemon should be about. All I wanna do it beat the gyms, elite four and become the Pokemon champion. X/Y, as much as I still like it just fine, is the worst when it comes to this. It's irritating when I finish a gym and am about to head to the next town, and then one of my annoying friends run up to me and say "Hey! Stop what you're doing and lets check out THIS thing!" or "Hey! So-and-so is about to Blah-blah-blah! We have to stop him!" How about no, and fuck off! I don't care! You know what I do care about? Becoming the Pokemon champ and being the very best like no one ever was!
Of the later games, though, I feel Black/White has the best story. I liked a few of the characters, I did kinda get invested in what was happening, and I got behind Team Plasma's motives, at least more so than whatever the hell Team Flare was trying to do (What were they trying to do, anyway?)