If time is an issue, I would strongly recommend day tripping for diving. I have used Scuba Iguana, and they are quite good. As far as lodging, check out the Sol y Mar. It is great.
The only advantage to a live aboard is that you get to hit Wolf and Darwin, which are great, but you also miss out on the land tours, which are even better, and some of the local dive sites. You will also lose two days in transit. With respect to the first post, I have found the day dive sites to be very good, and have some outstanding photos from these areas, including sea lions, mola mola, several shark species, penguins, etc. I am an underwater photographer, and Wolf and Darwin were not so good in the photography department: lots of nutrients in the water, and pelagics such as hammerheads and whale sharks too far away for decent shots.
The best trip we had were five days of diving with Scuba Iguana, followed by a six day Linblad Galapagos tour. Superb trip.
Have a super trip, and if at all possible avoid diving around a full moon: viz is lower with plankton blooming.