On one hand I enjoy the nostalgiac value of Red, Blue, Yellow, Gold, Silver and Crystal, and I enjoy that... for the most part, they were original. Some of my favourite Pokemon came from those generations.
On the other hand, I enjoy the updated graphics and gameplay (as in: New moves, new strategies, new combinations of types) that Ruby, Sapphire, Emerald, Pearl, Diamond and Platinum brought to the Pokemon world.
However, I dislike the old clunky graphics and animations of the old ones (not really a viable reason though, as they were made quite some time ago), and I dislike the lack of originality in the new games compared to the older versions.
So, I guess I'll have to go by the starters, gameplay and the storylines.
Grass: Venusaur > Torterra > Sceptile > Meganium. (4 for Gen1, 3 for Gen4, 2 for Gen3, 1 for Gen2)
Water: Feraligatr > Blastoise > Swampert > Empoleon (4 for Gen2, 3 for Gen1, 2 for Gen3, 1 for Gen4)
Fire: Blaziken = Charizard (sorry, I love them both too much to say that one is better than the other) > Infernape > Typhlosion (4 for Gen3, 4 for Gen1, 3 for Gen4, 2 for Gen2)
Total Points:
Gen 1 = 11 + 4 for completely original story + 3 for Gameplay = 18 (21 for FireRed/LeafGreen due to improved graphics and extended gameplay)
Gen 2 = 6 + 4 for the story still being pretty original + 4 for Gameplay = 14 (Haven't played SoulSilver/HeartGold yet, so that would probably add a good 5 or 6 points to Generation 2)
Gen 3 = 8 + 3 for story + 3 for Gameplay + 2 for improved graphics = 16 (17 for Emerald)
Gen 4 = 7 + 2 for story + 3 for Gameplay + 3 for even better graphics + 2 for Electivire (he's just that cool) = 17
So, going by that system, the first generation is my favourite, but to be honest, I love each generation of Pokemon for various reasons, e.g. I loved the first gen starters, and the extended "re-visit generation 1" addition to Silver/Gold/Crystal was just so cool.