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That is a tough one, because I really do go back and revisit each generation. I would probably say Gen 2 though, mainly Crystal. I just love everything about it. When it was added to the Virtual Console on 3DS that was it for me lol
I've replayed both FireRed and Sapphire a couple times, but other than that I mostly tried to stick to one save file per cartridge, so gen 3 is definitely my most replayed.
I don't replay games a lot, but my most replayed ones are probably Black, White, Black 2 and White 2 as I had all 4 games and it is my favorite generation.
I would haev to say Gen 1 with all of the different versions that come out. Very rarely do I restart my games because I like to try and max out the time on it so I can go back and see what no life I had. xD