I have to say I’ve got nothing inherently against the idea of a regional superagency, as they’re now contemplating in Boston. My beef with "Sound Transportation" here in WA is that it’s always been a stalking horse for Olympia to dilute Sound Transit’s power. It always comes down to two things: accountability and finance. That is, who calls the shots and who pays the bills. Often there’s an overlap between these two, but not always.
For example, if you have a regional entity, and its governing board is structured in such a way that the suburbs get a disproportionally large amount of seats, or the tax dollars come primarily from the suburbs, you’re going to get things like Metro’s 40-40-20 rule. In such cases, transit funding will suffer. But it doesn’t have to be that way. It’s all about how you structure it.
If this could be structured well, then it would certainly improve efficiency. They could have a single design department, a single group devoted to attaining grants, a central body to come up with standards and coordination, coordinated maintenance resources, but still break funding and voting up by appropriate geographical areas. We could even create a new transportation system (for instance the Seattle streetcar) without having to create a new agency.
My engineering firm has electrical, mechanical, plumbing, telecom, lighting, and fire code engineering groups. Each effectively earns money independently and there are many jobs with only, say, mechanical needs that don’t involve the other trades. But having us all in one company allows us to work together well when we need to, plus we can share just one group of administrative costs (billing, marketing, HR, etc.). The result is a much more efficient business model.