One of the problems is that the tax payers who will be subsidizing that new express Amtrak train, will complain loudly to their congressional representatives if their town is bypassed.
Its like many high speed train proposals. Yea, it is high speed until it has to stop every 5 miles.
Having raised the prospect of this sort of thing, in general, a few times in the past:
(1) There's a historical precedent for something like this in the form of the
Orange Blossom Special and the
Florida Special. In those cases, the model was mostly to run close-to-express from about Richmond to Florida (Florence was still a stop for the
Florida Special because of a crew change, but the 1941
Orange Blossom Special omitted all intermediate stops from the timetable). The issue is that you
only dropped about 30-60 minutes from the end-to-end run (24-25 hours became 23-24 hours) depending on the direction, etc. and in doing so you give up a slug of intermediate traffic. Bear in mind that on the current timetable, you only have a stop something like every 50+ miles between WAS and JAX.
(2) Even presuming that most traffic will consolidate within reason within Florida (e.g. Winter Park/Kissimmee to Orlando), you still have a rather good chunk of traffic that scatters among the various stations. Miami accounts for less than 1/3 of the South Florida traffic, and I don't think folks will "consolidate" from WPB to MIA (that's a messy two-hour drive involving overshooting on the train).
Edit: So, for a bottom line, I'm just not sure that such a train is viable. You'd probably get 80-90% of the timetable benefits from improving MAS on portions of the tracks from 79 to 90 or 110 and/or improving slow chunks to get the relevant MAS up closer to 79 (e.g. Baltimore, parts of Jacksonville). And you don't quite have the mass of ridership that you had in the 1950s.