Excellent analysis by Batfish.
I personally prefer my budget room (bigger than any boat cabin) on land to the fanciest cabin of the Aggressor. I also like to come back to land after a dive and have lunch and take a nap.
Boats like the Aggressor are necessary for diving in remote areas like Galapagos (esepcially Wolf and Darwin) and Cocos Island, but not for Manado area where most dive sites are five or ten minutes away. I can dive for a month (including air fare from the US) on less than it costs to spend a week on the Aggressor (without air fare).
Even when going on a day trip from Bunaken Island (both dives at the same place and lunch on board) to Popo which is an hour a way, it is a pleasant crusie along the coast, good chance to see dolphins and pilot whales.
To get to Catalina from the mainland here in Southern California it is typically an hour, so I don't consider an hour a long trip.
Where I dive on Bunaken (
http://twofishdivers.com/ they also have a resort at Lembeh Island now) , I have the flexibility of making as many or as few dives as I want and there is no artificial time limit on the dive.
I changed plans to dive a liveaboard in the Red Sea when I heard they limit dives to one hour. In Southern California on a day dive boat time is limited because the boat needs to move to another dive site and then has to get back to port. Most people running day boats in Southern California have other jobs and lives outside of diving unlike a dedicated dive resort like you find in the Manado area or a liveaboard. My dives in 2005 lasted from 70 to 100 minutes.
Be sure to ask a dive operations policy on length of dive and ratio of divers to guides. If it is eight divers to one guide, you don't have a guide, you have a "leader." There is a lot of small stuff to see and its hard when there is a lot of people trying to get a look at once.
Another plus for land based diving is that you are not fixed into a Saturday to Saturday itinerary.
Also a land based resort has people coming and going all the time and part of the dive tirp is meeting divers from around the world. I even ran into a couple who I had first met the year before.
I will be posting my 2005 Bunaken report very soon.