The jurisdictional creature that is the MMDA is under siege , mainly because of turf battles with the mayors of the component cities. This, I suppose was inevitable, given the growing power of local governments (spurned on by the empowerment given by R.A. 7160. It has also not been helped by BF's brusque administrative style.
I do wish that the HUDCC or Malacanang would weigh in on the need for a metrowide planning authority. So the city can find a happy balance between elective and appointive powers.
Why not have an elective metro planning council? Composed of representatives from each city who then get to appoint a director? Maybe malacanang can give them a share of tax receipts from the NCR as operating budget and they would be tasked with developing a long term planning vision for the metropolis? If the budget is substantial enough, they could provide counterpart funding to city projects that align with the planning objectives (including mass transit and the provision of housing.) Perhaps they could be funded from the road tax.
If the city mayors want to control traffic and clearance, then let them, but for the future's sake, we need to get beyond turf wars to a discussion of what Metro Manila will look like in the future.