I'm sure you will get plenty of differing opinions, but having been aboard Paisabatu II (the Wallacea boat), I can tell you that we did four dives a day, with the exception of our last day, when we did five dives. Yes, you can find budget lodging on Bunaken that is cheaper, but if you want to hit all of those N. Sulawesi areas, you are going to end up missing dives if you are doing transits between areas in order to do land-based diving.
I'm a casual UW photographer, so the facilities aboard the boat were fine for me. There was also a guy aboard who was shooting a Nikon SLR in an Aquatica housing, dual strobes, who had no problem keeping his gear maintained and serviced.
We did both land-based on Bunaken (Seabreeze Resort) plus the boat, and as I've said, we're scheduled aboard the boat again, simply because we really liked the operation. Definitely not a gold plate liveaboard, but clean, comfortable, well-maintained, and good food. Your choice. PM me if you have questions.