We, too, were just on the AOS (12/5 sailing). San Juan was fine. We arranged our own pre/post cruise hotel and our own air. Old San Juan was very beautiful as was El Morro. My only complain about the city itself was the slow service you encountered everyplace you went.
The ship itself was fine. The service was great, as always. The public bathrooms were always clean or being cleaned. Yes, there were large congragations of local puerto ricans each evening in the lobby bar (which were generally pretty loud), but if you didn't want to listen to it, there are plenty of other places to go. The windjammer was always crowded, but my beef with the windjammer is with Royal Caribbean, not with the local puerto ricans. If the windjammer is going to constantly be that busy, then put the staff up there to deal with it so that they can keep things restocked, including dishes and silverware, and while you're at it, see if you can make your food a little more appetizing.
The pool decks were fine. We never had problems finding chairs. Yes, there were the ocassional conga lines going on, but you could tune it out if you didn't want to listen. They weren't any more annoying than listening to the Bingo announcements.
And as far as what the local puerto rican paid for their trip...who the heck cares? I don't need to know what my neighbor paid, and they don't need to know what I paid. The important thing is that I enjoy the vacation that I paid for. If your enjoyment of your vacation is based off what the person paid next to you, then nothing will make you happy. When I go to Disneyworld, I don't stop to ask every third person if they are Florida residents and what kind of deals they got. I enjoy the parks for what they are, not how much I got in the gates for. I also know that there will always be resident discounts of some sort wherever I travel to. That's great for those that can make use of the discounts. Unfortunately, I am from Michigan, and we have no discounts, travel or otherwise (although I did attend the University of Michigan which gave me an in-state tuition rate which is half that of out-of-state tuition). Maybe I'm just used to the fact that there will always be inequities in life, but what a local puerto rican paid for their cruise isn't something to me that rates up there as something worth worrying about...
We liked our cruise, and the itinerary, so much that we re-booked the same cruise for the following year. For those that prefer not to travel out of San Juan, so be it. Enjoy whichever cruise you go on next, wherever it may depart from.