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1 = 3 > 2 > 5 > 4
Gen 1 gives me mad nostalgia, and I can play through RGBY any day and still enjoy every second of it, despite the obviously flawed gameplay. Gen 3 had probably my favorite region, and it was the turning point for the series in a lot of ways. Played through all three gen 3 games and I could easily do it again, in fact, I plan to nuzlocke Emerald after I finish some other things first.
Gen 2 is pretty rad. I like a lot of the Pokemon, and the games has a certain charm that I can't describe. I recently replayed Crystal and loved it to pieces, just as much as I did when I originally played Silver.
Gen 5 is pretty great since it changed a lot of shitty things about the series, and it added lots of conveniences. It also satisfies my pokemon breeding urges, and it introduced a lot of really cool pokemon, even though a lot of them were shit. I got White on release day and I still play it often.
Gen 4, I don't like so much. I bought both Diamond and Pearl on release day, and eventually got Platinum as well. I don't like the region, and I don't like most of the pokemon they introduced. It also doesn't help that the games felt so stupidly slow a lot of the time. I can go back and replay any of the main series Pokemon games, except gen 4. Mind you, I still enjoyed the games when they came out, but I don't like them enough to ever play them again.