I am referring to the state of the subway and buses under the NYC Board of Transportation, which was similarly a giant incompetent mess.
The distinction to make is that the counties and the City get to recommend the appointees for their slots to the Governor. It's a formality most of the time, but the Governor or State Legislature could tell the mayor or county executives to "try again".
As far as that last point, it's important to understand why the MTA was created in the first place; its primary mission is to dole out the goodies from the State and the tolled crossings to its subsidiaries. What they know about the system is at best, secondary to the job, since they are, by and large, not the people who run the system. That's why they appoint chairmen and agency presidents and all that.
The distinction to make is that the counties and the City get to recommend the appointees for their slots to the Governor. It's a formality most of the time, but the Governor or State Legislature could tell the mayor or county executives to "try again".
As far as that last point, it's important to understand why the MTA was created in the first place; its primary mission is to dole out the goodies from the State and the tolled crossings to its subsidiaries. What they know about the system is at best, secondary to the job, since they are, by and large, not the people who run the system. That's why they appoint chairmen and agency presidents and all that.