Your point is well-taken.
1) The MTA & NYCDOT will NEVER allow money to leave the system. Government agencies never like to see leftover cash because they feel that they will get cut back to the bone in subsequent fiscal years. So, your taxes won't go down unless it's an election year.
2) The MTA is not an agency that likes to change course. The agency KNOWS where new service needs to go. In 1993, I saw a report that stated that new transit services should run from Bay Ridge to Flushing and Fordham Center to Jamaica Center. This study was done YEARS before MetroTech and Jamaica Center took off. The MTA will only react when they can't run from something. East Side Access is going forward because NO MORE TRAINS CAN FIT INTO PENN. The X30 would not have run if Academy didn't pull out AND if a new company didn't attempt to restart Forest Avenue. Both of these projects are worthwhile, but none got done until they had no choice.
3) I'm not advocating for the MTA nor for NYCDOT to give up running existing routes that put money in the cookie jar. I'm advocating for allowing new private operators to provide a service that the MTA and NYCDOT could not or would not do. It's not usually a situation where the MTA or NYCDOT would do a route, except that private interest got in the way. It's a situation where MTA and NYCDOT say that the particular services aren't high on their lists, or "we don't see the demand for that service" or "we can't afford it". If a private carrier doesn't run a Bronx-JFK Airport route, it WON'T get done by MTA or NYCDOT either.
4) As you may know, NYCDOT is handcuffed. They can't do anything new to their route system. They legally cannot expand the bus system unless the city is in a state of emergency. They are still waiting on the authorizing resolution from the City Council. Now that the strike is expected to end today, the City Council will now resume saying, "What is a franchise bus again? Refresh my memory."
Your points are valid. Notice I do not advocate the same for Westchester County, even though they have plenty of holes there. Why? The Bee-Line system is a LIVING system. They will try new bus services and extensions. If after a period of six months or one year, those new trials are sometimes canned. Remember the 49 to Armonk? Parts of it now live on in Route 12, and the rest got canned. The 21 extension to Fordham Road lasted six months before it was canned. In 1990, both Playland-specific routes originated in the Bronx. Now the 93 is dead, but the 91 and 92 have joined us. The Bee-Line kept swinging the axe on a politically-connected BxM4D route that was wasting resources until they canned it and passed that equipment off to an exploding BxM4C. Route 84 must have been LOVED inside of the Bee-Line because they kept tweaking that route to keep it alive. When the route could not be saved, they killed it. THIS is the kind of attitude that we need to look at our transit system with. Frankly, trial and error is something the private sector is good at. It's also interesting to note that Bee-Line contracts with Liberty Lines Transit, which may or may not make trial and error cheaper.
There are visionary planners trapped inside of both organizations. They pay the planners to tweak the system and most of their suggestions reach the circular file. Many of these plans are high-quality plans that would make the system better. Unfortunately, private corporations do their best to serve the public, but must watch the bank account while doing so. The MTA does its best to serve the public, but its decision makers must adhere to their political accounts. It's easier to get the money.