Something that I think would help Jax make commuter rail more feasible would be to work with surrounding cities / counties. For example the city of Orlando is currently working on a plan to expand the Sunrail not only north and south, but east and west. We're working with the cities of Apopka, Zellwood and Deland. Also working with Universal and MCO to add additional stops at the airport and i-drive. Orlando would be providing most of the funding for the city expansions and Universal/MCO would contribute to their respective stations.
One "downside" of consolidation is that there aren't a whole lot of other governments to work with. With this particular corridor, it's really just Jacksonville and St. Augustine, with St. Johns County in-between. There also aren't
major destinations like Universal or the Orange County Convention Center along the line to help pay for it. One possibility I've thought about somewhat is that if this rail project were to create affordable standardized designs for its rail stations, they could perhaps seek funding from places like the Northeast Florida Regional Airport or Nocatee's CDD for infill stations. Won't be anything to the scale of the Orlando area deals but any money would clearly help here. And NFRA would have a lot to gain from having the only direct rail connection to both downtowns.
It basically boils down to what they are trying to accomplish. Intercity rail, commuter rail, heavy rail, LRT, streetcar, etc? All operate very differently. Since we're talking about a connection between DT Jax and St. Augustine, I'm going to assume commuter rail, as mentioned in the title (plus all options previously listed outside of intercity rail, really don't make sense for a +40 mile long route).
What do you mean the Express Select bus that runs 3 round trips a weekday isn't sufficient?
Commuter rail is a type of operation that is intended to connect commuters to a central city from adjacent suburbs. This type of services typically operates on existing freight lines or lines that were previously used for freight. Jacksonville's commuter rail problem is that not many people are commuting to the central business district from the suburbs and the suburbs are piss poor in terms of density themselves. I question the expense of establishing commuter rail on the FEC, because I'm not really sold we have the ridership potential or land use policies in place to support the system. Not because of the cost or time to work out an agreement with the railroad (which I believe is 100% doable).
Like I said, little about the FEC at this point demonstrates a disinterest in supporting rail provided the capacity increases are paid for. But I do agree, there's not a whole lot to say in terms of current TOD along even the existing FCF Blue Line that covers a third of the route. The development coming up at Avenues Walk has potential, but isn't really designed around the station anyway and features plentiful parking. St. Augustine of all places has shown some promise with the recent rezoning of the proposed terminus there, but similar or better really needs to be expanded all along the corridor. And more importantly, there need to be useful transit connections once you arrive at the station, since odds are your destination won't be the station itself.
Anything on I-95 is even more autocentric and low density, which is the exact opposite conditions needed for a successful commuter rail line. So your cost goes up to construct the infrastructure (you're building a new rail line and a new highway) and your ridership potential drops dramatically (i.e. the system is now operating in complete autocentric suburbia).
One of the problems with California High Speed Rail is that in addition to being a railway project, it's also a
massive highway project in order to create the ROW needed for the rails and then build all of the grade separation bridges. If there was no other choice, then you do what you have to, but Jax is not in that position for any likely regional rail corridor.
An interesting microcosm of this debate is actually the First Coast Flyer Red Line. People have long said that a transit line should be built along JTB so that they can access the beach, because people tend to get in their car and drive on JTB to get to the beaches. But when it actually came time to build a transit line, JTA chose Beach Boulevard, because of how much more sense it makes to run a transit line along that instead of JTB.
I still believe the most feasible option for any type of rail service between Jax and St. Augustine is either the extension of Brightline on the FEC or Amtrak running a corridor service between Jax and Miami down the FEC. Both are forms of intercity rail, as opposed to commuter rail. However, with the right placement of stations and timing of headways, the local community could use such a system for commuting within NE Florida.
It's the easiest option, I suppose. A city of our size is certainly physically capable of building regional rail, the issue seems to be whether it is politically capable of doing so. And as I think you've said before, it doesn't appear JTA is taking it all that seriously. I look forward to when the presentation they gave in St. Augustine is publicly available, though.
Again, it would appear JTA and FDOT should partner on this solution. Do you seeing them doing that or trying to go their separate ways? Of course, there is likely only room on FEC's ROW for one agency or the other so that may force them into a partnership eventually 
.
It would be ironic if not one, but two, of our designated transportation agencies get trumped by the private sector. Would further prove their inability and incompetence to take charge and vision the future.
The great thing about trains is that you can actually fit quite a bit on them. They're incredibly efficient infrastructure, compared to highways. Two or three tracks in South Florida (with three or four at stations) is sufficient for Brightline intercity trains, FEC freight trains, and eventually regional rail trains. The Brightline-only tracks in Central Florida won't even be fully double-tracked from the beginning, yet will still play host to 32 trains a day. And that's with everything running locomotive hauled on diesel (or LNG). With the political will to electrify and move passengers onto electric trains like in California, Europe, and Asia, you can move even more people or freight. There's no reason the FEC in North Florida couldn't host frequent regional trains, express intercity trains, and still plenty of freight trains.
To conclude this incredibly long post, I'm sorry to inform you that the private sector likely won't choose to act without public guidance. Brightline has generally followed public demand for where it chooses to serve. Remember that local governments have paid for most of the stations Brightline uses or will use, including Miami, Orlando, Aventura, and Boca Raton. They also were heavily lobbied by Cocoa to buy land for a station there. Looking especially at the recent changes in Orlando, they have to be asked to operate here, and it's unclear current leadership is willing to make that ask. Elections have consequences, even for the free market.
