Man... I don't know if I can pick a single favorite...
Emerald? It was my favorite for a long time, and is still among the best, but I find I can't replay it any more. RSE were the games (and Absol was the specific pokemon) that really made me wish for the physical/special split, and I can't go back now. But I still feel the urge pretty regularly, and at least spend some time there from time to time, just because it's such a beautiful region and such a great dex.
Platinum? I love Sinnoh - I think it's the most interesting region they've done yet, with a great variety of locations and stunning music to go along with them. And since those games introduced the physical/special split I wanted so much, they'll always have a special place in my heart. And Dawn is simply adorable. The dex leaves a bit to be desired though - some really good things, but too many just so-so ones.
BW? Great mechanics, great graphics, cohesive story, great dex. GREAT dex - I was so thrilled to see a game with an entirely new dex, with not one single tired old pokemon I'd seen a billion times before showing up in the game. And the new pokemon were not only new, but an awful lot of them are quite good, so there are a lot of team options. And reusable TMs is, IMO, the single best improvement they've ever made to the games. That made it so much easier to juggle lots of pokemon and be certain that all of them could have good movesets. I can only think of a few problems - I hated the way they forced the Dragon onto me at the end of the game. I went in there with a team of six pokemon because I wanted those six pokemon, and next thing I know this dragon is trying to force its way into my party. Yeah - I get it - legendary, stone, destiny, battle of truth and ideals, yadda yadda yadda... I still didn't want it on my team. And honestly - while N's castle is sort of cool in and of itself, the whole bit with it rising up out of the ground was just... silly. I expected to see Bowzer appear on a balcony. Those are pretty minor gripes though, and BW are the probably the games I've sunk the most time into.
BW2? - LOTS of stuff to do - Join Avenue, White Treehollow/Black Tower, Subway, PWT, studio, musicals (well, the last two are sort of cheese, but still). The expanded dex is... okay. As I said, I really liked the fact that BW had an all-new dex, so it was sort of disappointing to see all those old Zubats and Rattatas and Geodudes and such show up again. Then again though, Crobat is probably my single favorite pokemon of all time, and with a natural Acrobatics or a bred Brave Bird, it's even better than it ever was. Add in Roost from the move tutor. And the move tutors just generally - that was a great addition - I've spent an awful lot of shards on Ice Punch, Signal Beam, Hyper Voice, Dragon Pulse, Dark Pulse, Roost, Outrage... lots of stuff. And I love Join Avenue - not just running it, but being able to take advantage of it. And there are so many memorable moments - "Look for a big green hat," Elesa's gym, going through Reversal Mountain with Bianca and her awesome Musharna, fighting that Veteran with the Salamence out on Route 17, fighting all the gym leaders at the PWT...
Yeah... I guess, looking back, if I had to pick one favorite, it'd be BW2 - White 2 specifically, I think, for Braviary, old Opelucid and White Treehollow.