Really had to put my nostalgic feelings aside for this one.
#1 Gen 4 - Great soundtrack in DPPt, Sinnoh has by far the toughest Elite 4 in the games. The HGSS games were amazing and more than made up for what the GSC games had missing.
#2 Gen 3 - Best soundtrack in the franchise. Hoenn is the toughest region to date (tough evil teams and gym leaders), Battle Frontier was a great challenge, contests were simple and fun, and the remakes were a good rendition of the original RBY series, with their much-needed post-Elite 4 storyline.
#3 Gen 5 - I really liked BW, but B2W2 put this Gen up in #3. Pokémon World Tournament, White Treehollow (I only have White 2) and a great Champion with a great soundtrack to boot.
#4 Gen 6 - This Gen is the reason I bought a Nintendo 3DS. New Exp. Share is great but it just made it too easy to get through the Elite 4 (in the sense that I didn't need to do much training to meet the Champion with a party that was 7 levels up from hers). But so far I haven't seen much else to do after that. Pokémon Amie games are pretty fun, even though I haven't got the hang of it (and Super Training) yet.
#5 Gen 1 - Pains me to put it #5, but back then all the games were about beating the Elite 4 and completing the Pokédex, nothing else. However I loved the serious nature of the game: Lavender Town and the Pokémon Tower, the original Team Rocket's exploits, the soundtrack (specially the Trainer Battle Theme sounding like some fight to the death)...Kanto was awesome!
#6 Gen 2 - I liked Johto, but this Gen screwed with the good old Kanto I knew and loved. Screwed with the battle themes, screwed with the Viridian Forest, the Pokémon Tower, one of the underground routes, and most of all it screwed with Cerulean Cave. You never mess with Kanto.