I got into the series with Yellow, as well...except I never got out of it. Played the games, watched the show, got Pokemon Yahtzee, remember begging my parents for Charmander-scented cologne as a kid....yeeaahhh.....
My favorite games are HeartGold and SoulSilver, I'm one of the many who really loved Gold and Silver, and I feel the remakes really polished up already fantastic games. They're usually my recommendation for people wanting to get into the games, or just get back into them. My favorite spin-off would have to be Mystery Dungeon Blue Rescue Team. If I actually owned Conquest and got to play it I'd probably have to go with that though. I also really want to play Explorers of Sky, and the new one coming out for the 3DS.