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III, IV, and V for me, probably. DPPt and HGSS were both amazing sets of games that I had a lot of fun with. Same goes for RSE and FRLG. Unova was my favorite region and generation. <3
Gen 3 is my favorite all together. I greatly enjoy Ruby/Sapphire/Emerald, and FireRed/LeafGreen were my first games, even if they aren't my favorite it still makes them special. Also it had Colosseum and XD: Gale of Darkness.
Easily Gen IV. I haven't really enjoyed Pokemon since Gen IV ended; between DPPt and HGSS they had the perfect balance of new and old content. HGSS are the gold (haha) standard for remakes as far as I'm concerned, they offered everything you could ask for and more besides. The visuals were colourful and not too messy in the way that Gen V's were (although I'd blame that on the limited capability of the hardware) and the sprites were more expressive than the crappy polygonal models used in the 3DS games have ever been. Gen IV pushed the game mechanics forward by leaps and bounds, reintroducted some of the best features that Gen III took out, and had some of the best Pokemon designs. Also, the soundtrack. I could go on forever about the soundtrack.