Yeah, I think many of you are reading malicious intent into random noise.

Specifically with regard to the price of A-X-Y-Z-B with a redeye and an overnight when compared to A-B nonstop... usually the convoluted route is more expensive (for obvious reasons), and sometimes it ends up being cheaper (glitch, nonstop is really expensive, those flights are each really empty, etc). Especially because for given A-B there are going to be many such complex itineraries and your search is only going to unearth the one that is cheap. There is no reason and no benefit for AA to sell e.g. SJC-LAX-MIA-SJU with worse connections for cheaper than with better connections, unless the individual flights just happen to emptier, at less desirable times, etc. as compared to a "better" routing. And there was probably a poorly timed SJC-ORD-DFW-SJU you never considered because it was more expensive.