To each his/her own. I have been going to Cozumel since 1978, and while yes, absolutely, there have been some changes since then and not all of them have been for the better, Cozumel remains one of my favorite places on the planet. On every trip there, I start planning my next trip there before I leave.
I have only been out on a cattle boat for one dive, and that was enough; even as a beginner, the small boats (for me) were a better choice. I try to stay out of town in the middle of the day when there are a lot of cruise ships in port. I spend a lot of time over on the east side, which has stayed virtually unchanged in my nearly 30 years of going there (well, except for the devastation wrought by Hurricane Gilbert) . I stay in a small quiet hotel that was built in 1980 or 81 and is still as charming as it was then. I started diving there in 1994, and while I will grant that there has been a decline in some of the reef life in some locations, in my experience it has not been as extreme as some would let on; I still get amazing dives every time I go there.
I wish the cruise ship lines had never found Cozumel, but development is a fact of life. Sometimes it is up to the individual to figure out a way to turn chicken s**t into chicken salad. So far, I have been able to deny the march of development spoiling my experience on Cozumel.
As always, YMMV...