I could actually see Skywest putting a value on the 900 flying and AA saying it is too expensive and walking away (they DID just get a pilot group to agree to an 8 year concessionary contract).
My understanding was that AA got Skywest to do the -200 flying at a steal of a price, maybe even to operate at a loss for Skywest. They did that because Skywest knew those -200s were going to get parked and getting a carrier to agree to 50 seat flying when it is now the redheaded stepchild. With the -900s and other "Large RJ" airframes being the desired model of regional flying, Skywest can actually put a fair price on it, which probably shocks AA and thats why they walked away.
There are other -900 operators out there who could do it for less and thats probably why it fell through.
Just my thoughts.