Ugh, it looks like not many people play Alpha 3. The difference between the two Shoryuken supers is that the Shin Shoryuken is a 4 hit Super while the Metsu Shoryken starts off with an elbow to the stomach then a Shoryuken (Not sure about the hits, because the elbow usually knocks the person half across the screen.)
Shoryuken Supers come in many shapes and sizes. There are the Shin Shoryuken, Metsu Shoryuken, Shinryuken, ShoryuuReppa, Messatsu Gou Shoryuu, Shoryu Cannon and many others. If you click on the link above, the Shin Shoryuken is on the left and the Metsu Shoryuken is on the right.