I suspect that the best argument against lots of stops, at least on the first batches of trains, is avoiding short-distance traffic crowding out long-distance traffic. Density and traffic are likely such that at least on the "first go", traffic from Miami to various locations along the coast could block out MIA-ORL traffic.
A capable outfit manages such things by managing inventory. Not by simply not stopping at all.
Ehh...yes and no. "Not stopping" is a form of inventory management (namely, setting the inventory option for the skipped stop to zero), albeit potentially a crude one.
Let me step into the shoes of FEC's management. I'm looking at a report that says I can get a fairly high load factor on these trains at a rate of one per hour. I need to get service to within a given range of times (that is, I want trip times to be in the three-hour range) in order to attract business, meaning that I need to limit my stops as much as is practical. So I limit the stops I make as much as possible.
Moreover, those stops add to trip time...and adding too much trip time can force me to add a set or two to the route. Assuming an eight-hour cycle for a train (3 hours NB, an hour at Orlando, 3 hours SB, an hour at Miami), adding more than about 10-15 minutes to the schedule might force me to add one or two sets to the mix to make my desired hourly service. Those sets cost money (possibly $20m or more apiece, depending on the manufacturer and so on); further, those added stations also cost money. Of course, they'll also bring in additional revenue...but I might run into a space squeeze (through traffic being blocked out because of asymmetric short-haul traffic on one side of one stop or another), and simply put I might not be able to add enough additional passengers without lots of additional expense to make things worthwhile.
If I'm in FEC's shoes, I'm going to do the following:
-Miami-to-Orlando will be as we have it now, with a possible added stop in Cocoa. The problem with a Cocoa stop is that it's almost assuredly going to be a net addition for trains headed to/from Miami but not to/from Orlando, potentially gutting out a decent amount of traffic heading to/from Orlando. So I'm going to hold off there.
-If I find that there is room on the "shoulder" trains and/or off-hour trains, I'll add Cocoa but for Cocoa-Miami space almost as if it were Orlando-Miami space. Also, Cocoa won't be a stop on some of the peak-hour trains (again, managing inventory to zero on those trains). I'll probably need to have at least half of the trains make this stop to justify building a new station, etc.
-If the trains are completely full enough of the time, I'm going to have to weigh extending the sets (i.e. adding 1-2 cars), adding frequencies (which, aside from a possible "extra" at peak hours, is something I'm going to be averse to unless the operation is gushing money...I've got freight to ship, after all), or just not serving Cocoa.
-With respect to the possible Jacksonville extension, I'll add local stops on those since the Jacksonville metro area simply isn't as large (or growing as fast) as the Orlando area, let alone Orlando+Tampa...and that's probably going to force my hand on some of these trains. However, if I'm also adding Tampa, I'll probably be having to revamp my sets and order new ones to deal with added capacity issues, so I'm going to assume some sort of overhaul at this point anyway.
Finally, a worthwhile question: If the Tampa and Jacksonville extensions go in, what are the odds that Florida and the FEC seriously look at some commuter options in the relevant metro areas (with state/local subsidies to cover costs)? They're seriously looking at conneting Deland to Orlando as it is...why not Daytona and St. Augustine to downtown Jacksonville or Orlando/Kissimmee to Tampa and vice-versa? I know this is a long way off, but it does come to mind, especially given the chatter about Trirail options on the FEC.