I have been staying at BA at least once a year since 1987, through 5 owners/resort names. It isn't a mint-on-the-pillow luxury resort and it never has been. It has always been a bit rustic, but that does not bother me.Understand your dilemma, been there with group trips to Coz. BA is the most logical choice and ‘should’ be a no brainer. As long as expectations are communicated it probably is the right choice. It frustrates me that such a potentially awesome resort is so mediocre.
As for the turnover of personnel in the dive shop, the dive community on Cozumel is very fluid, pun intended, and DMs switch affiliation all the time, though some of the BA employees have been there for many years.