Hi Funscuba...
First, no liveaboards depart from the mainland. You fly to Galapagos and all but the Aggressor departs from San Cristobal. The Aggressor departs from Baltra. Flights are not included in the price.
The diving in the central islands (land based) and in the north (Darwin and Wolf) are like two different destinations. It is the north where you get the large schools of hammerheads, Galapagos sharks, silkys and seasonal whale sharks. I have often compared it to the difference in walking down a small town street vs Broadway in mid-town NYC. Yes, you'll pass some people in the small town, but the quantity and diversity of the north is far, far more abundant. For example, most reports this year are reporting 10-30 whale shark sightings in 1.5 days vs the excitement when a day tour returns from Gordon Rocks and sighted 1 whale shark. In the north is where you will see hundreds of hammerheads. In the central islands, you may see as many as a dozen and rarely 2 dozen, but a school of 6 is more common. The north is what put Galapagos on the map, not the central islands.
September and October are the peak of high season and sell out first followed by late August and early November. Those 12 weeks are considered the best diving of the year due to the presence of whale sharks, the large populations of hammerheads and the abundance of marine life. Hammerheads do migrate away between mid-late February, but return mid April. The populations are at the lowest this time of year. Northern Galapagos is the only place on the planet where you can dive with the bohemoth pregnant females leading some dive guides to refer to our whale sharks as Mrs. Big rather than the more common Mr. Big.
Two other great dive sites only accessible from a liveaboard are Cabo Marshall and Punta Vicente Roca. Though visibility can be quite low sometimes, mantas are almost always present at Cabo Marshall as are large schools of salemas, so thick, once a diver enters, the only way you know a diver is inside the school is by the bubbles coming out above the school. Punta Vicente Roca is known for mola molas, penguins, flightless cormorants and cold water. Temps can drop to 54 F / 13 C. Cabo Douglas is another cold dive site known for marine iguanas feeding underwater, a site quite uncommon on typical itineraries. You will see marine iguanas sunning everywhere, but to watch them feed is rare.
To get the most out of diving the Galapagos, try to go Sept - mid Nov. Rarely will you find deals during that stretch which is the peak of high season. The best deals onboard are usually during low season.
i've been told that you can also access the dive sites from the mainland's dive centres of galapagos but not the best ones, is it correct ? So the liveaboard might be the only option. But can you then join a liveaboard from the mainland of the galapagos ? Question to save time.