If you were in Houston, for example, you'd probably be a Continental (now United) elite. So who would you choose for flying out of Palm Beach or Fort Lauderdale? Maybe Miami too, but that's a lot farther away from me. Is either airport so notably better than the other as to skew this choice?

I'd mostly be either flying to (a) the west coast (SJC, PDX, or SeaTac, occasionally LAX), or (b) various points in the middle of the country.

If you don't plan on flying out of MIA often, there really isn't a huge advantage on any one airline. PBI pretty much will get you to the Northeast and some midwest/Texas hubs.
The only nonstops to the west coast from FLL are Delta (LAX) and Virgin (LAX/ SFO). youre going to have to stop at least once otherwise. (There is a FLL-PHX on US.)
Delta has the most destinations of the legacies, but if youre connecting anyway, probably not a huge difference.
The caveat is your "middle of the country" trips. Depends where they are. If they are DTW, MSP, or CVG, you're better off with Delta. If they are ORD, AA or UA, and DEN or CLE, UA.
If they're smaller markets, look to see who has the best onestop connections (IND, CMH for example are also Delta).

It looks like you'll be doing lots of connecting no matter what. If you want international award tickets, I suggest going with either AA (through DFW) or US (through CLT or PHX). If you have no interest in leaving the US, Southwest or Frontier might give you more bang for your buck.

I believe AA is your best bet, followed by CO.

Reason being, you can fly AS MIA-SEA direct yet credit the miles to AA.

You can also fly MIA-West Coast direct on AA.

In determining which airline(s) you would pledge your loyalty to, not only the flights you want to consider, but also the usage of the miles you will earn ... It depends on WHERE you want to go with your awards, and what kind of awards you most likely to redeem - to me, this is more important than the convenience of flights in making the choice of your primary airline(s).

I gather your question of which program you should use, stems from the thought that you would eventually use the miles earned for award travel... Hence I think it is better to look at it from the angle of award travel than the angle of convenient flights.

Of course if you fly enough, it is always better to have miles in different alliances.

We are primarily AA miles collectors, but we also collect miles in CO, UA and AS for example.