The first 3 and 5th generation games were compensated with via emulator, for I was either a) too young, b) too unknowing of Pokemon's existence or c) in possession of a broken DS.
Gen I: Red
Gen II: Crystal
Gen III: Emerald, FireRed
Gen IV: Diamond, later Platinum
Gen V: Black, Black 2, although I didn't play the two often
Gen VI: Well sadly, I don't have a Gen VI game, but I want X.
I really liked FireRed and Diamond over their other versions, simply because they had better Pokemon to choose from. I didn't really care for Dialga, but Murkrow and later Honchkrow was an amazing Pokemon. A lot of Diamond's version exclusives are amazing. Scizor and Tyranitar? Yes please. FireRed with Arcanine as a primary Fire type if you didn't pick Charmander? Amazing replacement. A lot of a person's preference is also based on the main mascot Legendary Pokemon, too. I didn't really like Dialga, but by the box it looked a lot cooler than Palkia, at least imo.
Hopefully that answered that last question there. :p