Gen I has not aged well. My main example of this:
It looks terrible, it sounds terrible, and a lot of the gameplay elements present in later games that make them run much smoother obviously don't exist. That being said, you really can't hate these games. Nostalgia and all that.
Gen II was pretty much the greatest thing ever.
Gen III had pretty terrible music, bleh graphics, a ridiculous story (I'M GOING TO BURN/FLOOD/BOTH THE EARTH). However, I really, really like most of the Pokemon introduced in Gen III even if they're rip-offs of Gen I Pokemon. It also made competitive battling kick ass, but really, nobody cares about that.
Gen IV was slow, clunky, and most of the Pokemon were lame. That being said, DPPt had pretty much the best evil-villain-team subplot of all of the games and it looked very nice. Wi-Fi Pokemon is a god-send, too. HGSS were pretty much the best games ever, though.
It's between III and IV. III if we count HGSS, IV if we don't.
None of the games are bad, though. I'm still a fan of all of them.