I personally think the game got better with every generation, but surely the most troublesome jump for me was from 2 to 3, because the new EV system and natures made it extremely annoying to play the story. A bad nature may make you not OHKO a threat and you may lose a battle because of it. I never cared for Hoenn, worst mapping in the series, and major wasted potential graphically speaking... Heck, when Crystal, an 8-bit game, looks good next to the supposed 32-bit games, you know there's something wrong with the graphics. Plus all the hiking that's necessary to get to certain places like Lavaridge and Sootopolis if you don't have Fly, and the attempt to stuff everything into one region. I prefer a coherent region like Johto or Sinnoh, not something that tries to be everything and fails at most of it. And, before I forget, the cutscenes with the legendaries were pathetic and primitive.
Qualitatively speaking, the jump from 3 to 4 was enormous. The region is better (my opinion of course but it has a degree of objectivity to it), the battle system started making sense for the first time, all Pokémon were actually given very good movepools... DP's faults are the slow battles and questionable Pokémon selection pre-E4, but IMO Hoenn had a worse selection because most of the then new Pokémon were worthless. Of course, you could get stuff like Flygon, but raising a Trapinch is a pain, and Vibrava's even more worthless.
Although I love 4th gen, my favorite has to be 5th gen. It's a gen I would keep replaying forever if given the chance. All new Pokémon during the story, but very few of them are bad. You can get by many parts in the game with stuff like Watchog since they actually learn USEFUL moves. Not like Hoenn where the early Grass-types couldn't even attack the opponent until, like, L20 or something. I just completed a Black playthrough, and the next time I could use different Pokémon and succeed anyway. The world is fairly simple, but in its simplicity lies its beauty.
So I vote the 5th gen as the best.