As Matt says, unless local authorities are willing to rethink zoning around transit stops, the utility of transit projects are greatly diminished. I'm not unsympathetic to local authorities who don't want to change, as plenty of people probably like their neighborhood the way it is and don't want radical change. Though, obviously, if you're trying to run a rail system from A-C, and B is in the middle you have a bit of a problem.
While I am sympathetic to people who don't want neighborhood change, I do suspect that for something like this opposition comes from people who have an exaggerated sense of the horror that is a walkable neighborhood with a bit of mixed use residential/retail.