Personally, i think it's:
1.Gen 3 (there's a lot of factors that made me decide this but the most important one is the very fast and smooth gameplay most GBA games had, and most DS games didn't (Gen 5 being one of the few exceptions, which is why that's my 2nd favorite))
(I know I'm gonna piss off a lot of genwunners with the Gen 1&2 placements, but i honestly think those games aged very poorly)
Best Pokemon game is Pokemon Emerald (Dat Content (Battle Frontier, Deoxys, etc))
NOTE: Gen 6 is excluded since it's way to early to judge.