I have been diving in PV a number of times and will be back later this month. For what it is worth, I have always used Vallarta Undersea (and predecessor Pacific Scuba). I have always had a good experience and particularly like the location as their shop is located near where I stay in the Marina Vallarta area. The main thing to understand is that a few shops (Chico's comes to mind) take out large cattle boats which may include snorkelers, which may be good if you are a group of divers and non-divers. Most of the boats in PV are 6 packs or smaller boats and lack amenities you may be used to in the caribbean (ie lack of bathrooms, large wash bins for cameras, etc).
Nearly all of the mainstream dive sites are within the Bay of Banderas. The most popular dive site is Los Arcos and quality of the dive can vary widely based on time of year, recent weather and number of divers/swimmers. Other popular sites are Majahuitas and Marietas Islands.
End of the day, I enjoy diving in PV. I would not head there as a dive-only trip, but I always try to dive when I am there. Happy to answer other questions, but hopefully gives a good overview.