You should read the article released by the Boyd Group as well as watch the video from the Mesa TA road shows. While your questions aren't specifically about Mesa, it details a lot of the scope and financial issues facing regional airlines.
I have friends at AWAC. They are a great regional to work at. However, I do fear for their future and ultimately the future of the 50 seater in wide use. I do think some airlines will continue to fly them, however most will eventually go away.
Ultimately, over the next 5 years, regional airlines will shrink. Some will merge, others will disappear altogether. At this point, I don't think it is a matter of one regional's feed costing their mainline partners more than another. I think it's more about who can attract pilots to staff the flying, and ultimately who isn't flying primarily 50 seaters. Working for a wholly owned American regional is probably guaranteed job security for the next 5 years at least. At least that is how it appears right now. Many of the non-wholly owned regionals may have a more difficult time hanging on to contracts in the future.