I don't understand what people were expecting GGPO to do. If your connection sucks, your ports aren't forwarded, or you play people with bad connections it will be bad. No netcode can fix that. As it stands the netcode is a lot better than SF4/Marvel. AE is ok if people are close but playing vs people cross country is unplayable. The rewinds, weird graphical glitches, and so on that ggpo introduces, at least to me, is much better than input delay.
I've only been playing sets with people in private matches so I don't know about the matchmaking but I hope it gets fixed.