We really don't see much of a change since AE pulled out. We always fly to Beef, buying all of our flights on one ticket: American, Delta or United. Jet Blue also works if they serve your city. They all partner with Cape Air or Seaborne. The ticket prices are reasonable, if you don't fly on a prime day, because the airlines have gotten really good at maximizing their revenue - good for them!
If you are flying Southwest to San Juan, then, yes, the connecting flights can be expensive. Try InterCaribbean. You can usually save money by coming in late, staying at the airport and taking the early Seaborne flight.
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