In many areas this would effectively lead to the suburbs being able to dictate urban policy to the inner city, where suburban commuter interests like parking override the interests of the actual residents. The 1998 amalgamation of Toronto is a good example of this happening, and I think a lot of Old Toronto voters are quite unhappy with this, given how it led to mayors like Rob Ford who would never have been elected with the old boundaries.
Other areas try to solve this by creating an uber transit authority which theoretically directs and coordinates the smaller agencies for the greater regional good. A good example of this is the Regional Transportation Authority in Chicago. It often doesn't work out the way it's intended (in Chicago, the CTA [city proper transit] and Metra [commuter rail] still have very poor coordination, although Pace [suburban buses] and CTA do have somewhat good coordination).
A third approach is to (try to) make the whole region's transit the responsibility of one single agency. Picking Atlanta as an example here (MARTA), it tends to lead to affluent suburbs (Cobb and Gwinnett Counties) trying to stay out of the system because of concerns like "transit brings crime" and "it's too expensive and no one will use it" and other assorted nonsense. So that approach has its problems too.
In short, this is a very thorny problem and there honestly aren't a lot of places in North America that do it very well, although some are worse than others (the SF Bay Area may seem like a mess, and it is, but it's inarguably better than the dozens of barely-funded, not-at-all-sufficient systems that exist in most large and medium cities in the U.S.). I think the right solution is probably specific to each region and it still won't solve every problem, at least not without a level of funding that transit simply does not get on this continent.
