Needs less third gen hate and moar fourth gen hate.
To be honest, I can't choose between the first three gens. It really depends on which one I've played most recently, and as such, the one I recall most vividly.
I love first gen's simplicity, the fact that it started it all, the originality in Pokemon and their sprites, the music, the whole Unknown Dungeon -- a concept which has yet to be found in future games, I believe -- the game had a lot of great stuff in it, truthfully. Was the gameplay perfect? No, far from it. But it's still awesome. And some of its flaws, like the glitches, are what make it so memorable and awesome to this day.
Second gen...arguably has the biggest nostalgia for me, actually. It doesn't make sense since first gen was the first I played, but looking back I recall second gen MUCH more than first. Nonetheless, first to second gen is almost as big of a transition as SSB64 to Melee. Night/Day, registering items, breeding, easier use of HMs, new types, experience bar, another region...I could go on and on describing them all. The gameplay just felt...great. MK's right, there's SO much diversity, and you can catch nearly all of the Pokemon in the wild. Also, the plotline of G/S/C is by far my favorite. Team Rocket is definitely the best evil organization (they're just evil, no stupid ulterior motive and then turning soft when their plans go wrong *COUGH*EVERYTEAMAFTER*COUGH*), and I liked how Team Rocket was really involved. They start out with just taking Slowpoke Well, and work their way all the way up to taking over an entire Radio Tower. And Lance, who is simply bad***, is there to aid you. Well, sort of. But he's still sitting there being bad***, regardless.
It felt like G/S/C had the MOST content without just slapping on replay value on the end. Which is great for perfection or if you're bored, but...otherwise it bores you. 251 is a perfect number for the Pokedex. Enough that it's a challenge, but not so much that you have to break it up into many pieces lest you shoot yourself out of boredom.
Third gen...everyone hates it, and I can see some reason to that. It did take out the whole time system and the extra region, both of which people were especially butthurt over since it was the first to remove them. But Hoenn is, quite frankly, the most diverse continent, and for that I love it. It has rainy forests, beaches, islands, cities, deserts, caves, ash-y plains and mountains...it's immense. NO other gen has quite so many environments. My favorite part about this gen, though, is that it felt like a fresh start to me. First gen and second gen fit together pretty well...but third gen feels like Pokemon in a whole new...everything. Which might seem bad since the first two generations were good, but something about that just made it amazing. And for all of its crappy Pokemon, I found a lot of them actually intriguing. When you think about it, third gen brought a lot to the table too. A ton of graphical upgrades like visual PC boxes rather than the text-based ones, running shoes, etc. I loved that generation, unlike most of the population.
Fourth gen, you usually either love it or loathe it. I feel the latter. I like the physical/special split. The graphics are nice. But in the end, the plot feels lackluster at best with a crappy team which feels more like Jessie and James from the TV show, weird hair included. Overall...it felt very bland to me. The gyms were pretty creatively designed, especially the overhauls in Platinum, but it doesn't make up for the rest. Yes, there are 493 Pokemon to get, but that's not really replay value...completing such a massive Pokedex is painful and annoying. Also, I feel like fourth gen doesn't get the flack it should for not having another region, since I feel like a lot of people disliked third gen for that. People hate third gen for not continuing it and then I guess the issue stays third gen's. Most of the Pokemon are unimaginative and crappy. Platinum has slightly bettered my opinion on the generation, I do think Galactic is a little better there and is more fleshed-out. Until Platinum, I hadn't listened to the music that closely, and now realize that a lot of the battle music is really good, especially Cyrus and Cynthia's themes.
I think when it gets hated, fourth gen will sometimes receive more hate than it deserves, but it gets more credit than it deserves too. Purely mechanics-wise, fourth gen does win, yes. HOWEVER, when you talk about generations, you're generally referring to the games in their entirety. There's not much point in discussing the mere battling aspect, as few could/would argue that fourth gen did not better it. A lot of people seem to settle on fourth gen as best simply because of mechanics. If you like it the best, feel free to do so, it just irks me when people do it for reasons that seem illogical.
So I pretty much have to go with...
First = Second = Third >>> Fourth