Honestly though, I don't understand why they didn't just release the most suped up version of the game, as opposed to offering the earlier versions without all the added characters...other than that they're probably trying to squeeze $$$ out of us...
Welcome to the world of Street Fighter. *puts aside some cash for the upcoming Super SFIV*
I haven't been keeping up with any of the Street Fighter releases on VC. Confusingly, they've seemed to have made available both Genesis AND SNES versions of each game..... which is something of an oddity, since it's widely believed that the SNES versions are the superior ports overall.
Having never played the SNES version, I can't vouch for Alpha 2 -- but yes, be aware that the Alpha games are a different beast than the "II" games, so it shouldn't really be considered when looking for a definitive, "complete" version of Street Fighter.
That said, if you're looking for the definitive version of Street Fighter II, my money would go toward Super SFII for the SNES. It's got the full sixteen character roster, turbo speed settings, and, as Jay says, tweaked gameplay balancing and added moves.
Turbo Hyper Fighting for the SNES is another consideration, and the one I prefer most of all. It's the SNES counterpart to the Genesis Special Champion Edition, but again, with better graphics and sound. This one is cool, because you can choose to play with either Champion Edition or Hyper Fighting gameplay tweaks. (For instance, the CE doesn't allow for midair Hurricane Kicks for Ken or Ryu, while Hyper Fighting does.) Plus, I just dig the beefier sound effects and older gameplay mechanics, like the hurricane kick traveling horizontally midair, instead of the upward/downward arc that it does in SSFII.