Alpha 2 has superior fighting mechanics, Alpha 3 has better music, character selection, and single-player modes. Competitively I'd rather play A2, for fun I'll take both.
I think Alpha 2 is the better game, gameplay-wise.
Alpha 3 is a mess if we talk about balance / bugs, but also had more characters, world tour mode... I can understand why some people like that game more than A2.
Yup, but Alpha 3 will be favored by those who aren't competitive or all serious about their fighters. It's got very solid single player content along with the best and biggest roster outside of SFIV. The game simply doesn't hold up competitively speaking because of crouch cancelling in v-ism.