Check out this video,who even did this did a really good job,Im very impressed. http://www.ebaumsworld.com/2007/01/scorpion-vs-ryu.html
Here's the full version: http://uploads.ungrounded.net/276000/276650_MKvsSF2.swf (http://www.megaupload.com/?d=EC3ULN0B) Kinda makes me wonder why if Marvel vs. Capcom was such an obvious idea, why the hell didn't they ever make a MK vs. SF mashup?
Capcom had made the stand-alone Marvel based fighting games. Hence, the fighting styles were similar enough to adjust to work within the same game. I personally feel a MK vs SF game wouldn't work, due to the games not quite controlling the same.
Posted this a while ago: http://www.assemblergames.com/forums/showthread.php?t=8914 Very cool video, and yes, the ending is disappointing...