I put down Emerald, because it was my first Pokemon game I ever played, I replay it all the time either on my GBA slot in my DS or on my emulator, and because it offers some pretty challenging post-game content that I still haven't beaten yet.
But on a more objective basis, it's more like a 3-way tie between Emerald, SoulSilver and Black 2.
Emerald has a huge nostalgia factor for me and I really like the designs of the Gen 3 Pokemon, second only to the first generation, plus Team Aqua and Magma were just hilarious to watch fighting each other; but it's not the most balanced game out there, I mean half of the region is water (fitting for the theme of the game, but still a pain in the *** to travel on).
SoulSilver is really nice in that you can travel in both Johto and Kanto, you can fight all the gym leaders whenever you want, but Team Rocket is even more pathetic here than usual, and it's really not all that hard, the most challenging region doesn't even have Pokemon above level 50 for cryin' out loud.
Black 2 has some issues. I really don't care for a large portion of the new Pokemon, and I can definitely see a decline in the designs as of late. I also really don't like how the game just blocks off the path to 3 whole regions, I mean I get that they want you to explore the regions after you beat the Champion but some of the methods they use to do so are pretty freakin' stupid. "We're all gonna dance here and block your path, and we don't know when we'll stop." Seriously GameFreak?! But on the other hand... I'm really enjoying my playthrough of it. It's much more challenging than what I'm used to, the wild Pokemon are higher leveled and the trainers are smarter in how they fight. While I may not care for a lot of the aesthetic designs, the strategy has definitely improved, and the new type combinations are really cool (electric bugs, golems, and ice dragons? Awesome!) While I haven't delved into the PWT that much yet, once I beat the Champion that's pretty much all I'm gonna be doing.
And I'm just gonna say it now, Team Plasma is my new favorite villain. They have far more of an impact on the world and the people in it than past villains; even 2 years after they disbanded the effects of their actions are still felt. I personally like Colress because he's a scientist through and through, making all of his decisions based on what would bring out the potential of Pokemon in the most efficient manner, appealing to my engineering instincts (also he kicked my butt when I faced off against him, anybody who can do that to me gets respect from me). And Ghetsis... oh man, Ghetsis is a monster. I don't even need to go into why that is, also I don't want to spoil it for anybody out there who hasn't gotten to THAT part.
So yeah, tie between those three.