Available capacity is no excuse, in the eyes of BNSF. They can't pass up any opportunity to feed at the Public Tax Dollars Trough. Of course, most improvements benefit their freight operations far more than any Commuter Trains. The same folks who held out their hands @ Amtrak / Caltrans any time another San Diegan was proposed, did the same thing here in Seattle to Sound Transit. And lets not forget selling an entire line to the Railrunner people in Albuquerque. You think BNSF LOST money on that deal ???
I agree that the Valley of the Sun has severe growing pains & urban sprawl in 3 directions; the light rail is a start, even if the route is dubious. Why not follow Portland's example & put the tracks alongside or in the middle of existing freeways ??? It would work on I - 10 & the 202 Loop.