It all started, obviously, with Street Fighter Alpha. I really liked Alpha 1, especially the ability all characters had to perform chain combos. Alpha 2 took away chain combos and made the general gameplay feel more SF2-ish. There was one major difference: the introduction of custom combos, possibly to make up for the loss of chain combos. Custom combos made supers basically obsolete, as supers dealt less damage in most cases. Also, in certain situations, a properly-timed activation would lead to a completely unblockable combo. Alpha 3's take on custom combos, V-ism, was an even greater threat when combined with the new air-juggle system.
When you trace its heritage, you can see how the Alpha series evolved into something very different from the game it began with. Alpha 3 came a long way from Alpha 1. But even with all of its quirks, Alpha 3 can be fun to play, as it is certainly a unique take on the Street Fighter formula.