It's the way of the world. Travel has changed substantially over the past couple decades - populations have increased, things have become less expensive and easier, emerging middle classes in some large countries (China & India, to name a couple) have allowed access to travel by billions who could previously only dream of travel as a "rich man's" luxury - not any more. Popular places are super-crowded (been to London or Tokyo lately? I have - they're quite different than they were when I did my post-college backpack trips). I was in Palau last year at this time, and the place is very crowded with Chinese tourists. I spent a week at a tiny island in southern Thailand in October (hard to get to, not super well-known). There, too, Chinese tourists were everywhere, and development was booming. Cruise ships have become a mass industry. Like it or not, the world loves to travel. It is what it is. You have to work a LOT harder to find those sleepy little towns now (they still exist, but require much more work to reach them before the 7-11s and the cruise ship piers go up).
My first trip to Cozumel was in the mid-1980s. Yeah, it was wonderful. We saw one or two cruise ships in our time there. I've been back a handful of times since and the changes are obvious (I go every 5-7 years, so the changes are hard to miss). Is it still worth going? I'm flying there tomorrow, I'll tell you in a week, but it still is easy to get to, has lots of things to offer, and the annoyances are (I think) still below my critical threshold.
Every place is a mix of good and not-so-good. If there are any better (easy-to-get-to) places, I'd love to hear about them. But right now I gotta go pack my dive gear, my flight to Cancun leaves in about 16 hours...