I understand that they can't divert the money directly, but they haven't even funded it entirely yet. We all know that in politics, regions have unspoken quotas of capex they can have. In this case, New York could spend 6 bil on this, which would be all well and good, but they could also use their 'allotment' on something more cost effective, like getting a grant to replace sewer lines, update the water system (and finally finish CWT3), rationalize the city's grid, etc.
As for the argument about minorities, point taken, but you could instead target some of the above listed monies at such neighborhoods. Already we're seeing this strategy with the 125th st terminal rather than a bx extension.
I really do think sometimes that the best thing that could happen to the MTA would be lots of republicans in the state and city govts. I'm a democrat through and through, but it'd force them to cut costs.