I think this sort of regional commuter rail puts the cart before the horse. I think it would be best to start with local light rail and then tie into this the commuter rail system out into the hinterlands.
I think rail is so diverse, it should not come down to a traditional light rail (ex. Dallas' DART) or commuter rail (Nashville's Music City Star) option for Jacksonville. Instead, I'd suggest studying the potential of a hybrid system, such as Austin's Capital MetroRail or New Jersey's Riverline. Both of these systems have trains operating on freight railroad tracks. They also provide service like light rail in denser areas of their communities and act more like commuter rail out in the hinterlands. Incorporating such a system in Jacksonville would allow us to eliminate portions of the BRT plan, saving hundreds of millions of dollars, without having to spend more constructing a parallelling traditional commuter rail system, as proposed by JTA.
RiverLine route map
In Trenton and Camden, the RiverLine provides light rail like service with several stations located within blocks of each other. However, in the rural areas between it acts more like traditional commuter rail with stations spaced far apart.
Austin MetroRail
Capital MetroRail (currently under construction) incorporates the same "no-frills" ideas to cutting down implementation costs, while putting a different type of rail vehicle and service on their existing tracks. They call their hybrid commuter rail system "urban commuter rail".

This is a good way to get something up and running in a relatively short time frame if you live in a community facing a budget crisis that may not be willing to pay for the additional costs of dedicated right-of-way and electrifying lines across Jacksonville from the start.