My take:
Personally, the state should just let
JR Central assume total control of the HSR route--provided that the French, Koreans, or Chinese don't come up with better plans.
Simultaneously, FDOT should form a rail authority to operate in-state corridors. The state should definitely take a clue from NC and and staff attendants at certain suburban stations and tourist towns deemed too small to have a full-time agent. While Amtrak might have a prearranged agreement for FEC service, the state should strongly consider other entities for the other routes while it would be understood that connections would be coordinated by the various operators.
If Florida follows my advice to a tee, then Jacksonville Union Terminal would be the city's hub while a new North Jacksonville station will be built for commuters and the planned Sunrail LYNX station will be the main Orlando stop. If it looks west to California, then a hypothetical Amtrak Florida would use both the existing station in JAX and Union Terminal and would use Orlando's current Amtrak station as the city's principal stop with several suburban stop to avoid overcrowding.
These maps show how an effective intercity rail system can--and should--be built:
The maps are based on a blog
entry that I did earlier this year.