They did face scans, but they still redesigned and tweaked them, so that the faces look unique and not exactly like a specific person. Superman for example is based on Henry Cavill, because he
is current Superman, but they altered in-game Superman's facial features just enough so that he feels unique to Injustice...and so that they don't have to pay Cavill millions.
The facial animations are also done by motion capturing real actors. You can instantly tell by the high quality:
In general you clearly notice that this game cost a lot. Production value that no other fighting game this generation can match. But NetherRealm fighters usually sell really well, so they are getting their money back thrice.
Regarding the stages...they are actually the real highlight for me. I've never seen so pretty and detailed stages in any game, with so much going on, so much interactivity, so much breaking, such pretty lighting and then those seamless stage transitions. O: