Like many others here, I grew up with the 1st two generations, in fact, Pokemon Blue was my very first game. So I was really torn between the two, I love the mechanics and upgrades that came with G/S/C, but I love the Pokemon and story of R/B/Y much better than 2nd gen's story and Pokemon.
I voted 2nd gen because, while the story and difficulty were lacking (admit it, Team Rocket and the level of your opponents were pathetic) I really loved those 3, those were the ones that I played to death, literally, my Gold is dead now, my sister's silver is dead, and my Crystal's time is all screwed upped. The day and night features and the new Pokemon as well as many other features, are what made this generation so great. Even if Kanto was watered down greatly, it was still nice to go back & see the changes (I still hate what they did to the Viridian Forest though). And being able to face Red was a real bonus. Funnily enough, while for me the trend is that the 3rd game in each gen has always been my favourite (Yellow, Emerald and Platinum) with Crystal, this isn't the case, even though it touched upped in some places, I never really cared about Suicune, I prefered facing Ho-Oh in Gold.
The 1st gen comes in second because it had the most originality. The original 151 Pokemon were the best, the music was awesome (I still whistle the bike tune) and the evilness of Team Rocket (and I don't mean crazy environmental
ist or a nutcase who wants to create a new world) kept me determined to stop them. And Yellow was and might still be my fav of the Pokemon games.
I'd say the 4th gen is third because I really love Platinum's story and look. And I say Platinum on it's own because it did a lot to Diamond & Pearl, I don't think I can go back now and play my Diamond. The way they filled in the gaps in the story and made Cyrus even more demonic, plus the good old animation and other features that were fixed upped makes this one a contender for my fav. Although, the reason it's falls behind the others is that it's lost a lot of the old originality and it has so many Pokemon that I really couldn't care less about catching em' all anymore. Plus the Pokemon are no longer nice or cool, they're just there. On the flip side, this is the generation that will have the Gold & Silver remakes, & if they turn out good, I might have to change my mind.
So that leaves the 3rd generation. Even though Emerald was my favourite for a while (Rayquaza is awesome) I still feel that this is where my love for Pokemon started to slip. Even though the lands and stories were getting better, I just didn't care as much in this one. This is when I originally thought that they had gone overboard with the number of Pokemon, the most I did was catch the required 200 in Sapphire and Emerald, and since I had spent 300 hours in total on Emerald, I said screw the last 100 whatever Pokemon. I also didn't care for the setup of the gyms, for example: in Ruby, you catch a ground type legendary...then you go face a high leveled water pokemon gym...But I did like what Emerald did story wise: infilitrating both HQ's and watching Rayquaza intervene in Kyorge and Groudon's fight was cool.
All in all, I'd say I love them all almost equally, but I didn't select that because I knew generation 1 and 2 were the obvious winners, with the features of 2 beating the originality of 1. Either way though Pokemon FT2ndW, with Zelda being the first win still