All that aside, it'd make perfect sense to use Wanda as the whole Civil War schism is over dealing with people with powers and aside from Banner, she and Quicksilver are the only movie characters this will directly apply to (Thor doesn't count for obvious reasons.)
It actually applies to just about everybody, in the end it's a right's issue. In the comic book story Stark used his position as SOD to call for the registry of all people with superpowers and either they registered and singed with SHIELD or by put into a prison made for them. Spider-Man and Wanda are directly affected by teh superpowers registration act, but it does affect many others as well.
I didn't say it didn't affect anyone else, I said it directly affected Wanda because she's "enhanced" and to date, she, Cap and Banner are the only movie characters to fall under that category.
If they're going to show the direct consequences of the registration act then at least one person the audience cares about getting the sharp end of the stick is something of a must, no? Otherwise it'd be like having a historical movie about civil rights in the US southern states without any southern black people in it. They're kinda the whole point.