I haven't really seen a good case for treating them (Alpha vs Alpha 2) as separate games when the content of the sequel is mostly made up by the content of the first part. They strike me more as rolling updates to the base game with a few fighters added and the combo systems changed up or improved. Alpha 2 seems like a bigger leap from Alpha 1 than the various 2 varieties but they still add less than your average Civilization expansion pack and we haven't included them. Or say the REmake. That it's a stand alone release doesn't really mean much to me given the arcade roots of the franchise and the only way to do a significant update was releasing a whole new cabinet.
I completely disagree.
I feel like that would be playing into the whole "caring about historical impact/progression rather than the best overall product" thing that I mentioned earlier. On top of that, if we only wanted to count one version because they're too similar, I tend to lean towards going with the final iteration rather than the first iteration. Although I happen to prefer Alpha 2 over Alpha 3 in this case.
Street Fighter in general tends to start with an incomplete product and flesh it out after seeing how the base performs. I think it would be very unfair to the franchise as a whole to only judge it by what would end up being by far the crappiest version of each.
World Warriors, Alpha 1, and New Generation are not particularly great games-- they're all very flawed, and probably wouldn't be too rewarding to play today, but the final versions of each of them are pretty damn brilliant and are what allow them to hold up over time (and maintain a healthy tournament scene), IMO. I disagree that the newer versions are just added side-content. The balance/mechanics tweaks make a world of difference and fundamentally changes the games for the better (especially how they feel) in all three of these instances. If it stopped at World Warriors, Street Fighter II would be historically important but would rightfully be seen as severely dated and feel sluggish. Which couldn't be further from the case-- Super Street Fighter II Turbo is as strong as (in my opinion, superior to) any modern fighting game released today, for my money.
Despite re-used assets (and keep in mind, the amount of work and talent that goes into creating the assets in a 2D fighting game is kind of nuts compared to other genres), I would argue that the jump from Alpha 1 to Alpha 2/3 as well as the jump from World Warriors to Turbo/Super Turbo are closer in significance to the jump from Megaman 1 to Megaman 2 (which would be a travesty to rate the former over the latter).
If your suggestion was flipped around, that World Warriors/Alpha 1 should be excluded from these polls because Super Street Fighter II Turbo/Alpha 2 & 3 exists, I could get on board with that.