Who you go with depends on where you want to go and when you are there. Most local shops operate on a schedule: Mon is Dive Site 1. Tues is Dive Site 2, etc. If you are an advanced diver, I doubt you would be interested in Academy Bay or Santa Fe. If you are not an advanced diver, you wouldn't be interested in Gordon Rocks. If you're a macro photogapher, Cousins is great. Penguins at Bartolome, etc. So it totally depends on what level you are and what you want to see. And which days you're looking for diving.
Hammerheads are usually at Gordon Rocks, however, 2 weeks ago, there was not one to be spotted and yet, I saw over 100 at Mosqueras. I would recommend hitting the 3 sites at Floreana if possible as the Park may soon close Diablo del Corona (Devil's Crown) to all but some of the cruise ships. It's an easy dive with lots of life, but the point is that you may never have the chance to dive there again.
By September, it is possible that new permits will be in place. Price is another consideration. Lots of local options. To me, a big deal is engines. To go on a slow boat with 2 stroke engines getting you sick from the fumes is NOT my idea of a good time. I've gone from Puerto Ayora to Gordon Rocks in less time than it can take some boats to go from the Canal (after a 45 minute drive in a taxi) to Gordon Rocks.
Am slowly adding more about sites to my blog: divingthegalapagos.com