Well, any time the government gets into micro-managing salaries, the whole thing is fubar, guaranteed. The problem is that the government decided that there was a shortage and decided to start tinkering with employment levels, which set off the chain of events leading to this kind of discussion.
Anyway, you make a good point about cost of living issues, so some sort of local indexing would be a good idea.
To me, the most important thing is that we include other professions in the "market rate". As it stands, even if H1Bs pay market rate, they can still put a damper on wage growth, while other fields without extensive guest worker programs sprint ahead. So I'd say "if there's indeed a shortage, what other professional degree paths are getting these students?" So in this case, they'd need to make sure that grads of top engineering schools who get visas are not paid significantly less than grads of comparably ranked law and business schools. This would protect against the use of visas to cause wage stagnation in engineering relative to other professions.