Mermaid IKomodo, Raja Ampat, Ambon, Banda Sea

The 15-day Biodiversity Cruises on Mermaid 1 and Mermaid 2 are the world's best liveaboard dive trips. Twice a year the boats reposition between Raja Ampat and Bali and offer this 1500-mile journey through the Spice Islands with about 45 dives. (True believers can continue from Maumere to Bali for another week). The dive sites include all the natural diversity of the Coral Triangle-- walls, bommies, muck-- and offer a wealth of big pelagics, macro, hard and soft corals. No wrecks.
IMHO Mermaid is the best combination of quality and price in the region. The rooms, food, and service are resort-standard, and the dive operation is superbly run. The boat is a steel-hull twin-engine, which seems to me an excellent thing for remote waters. Because the cruise involves several open-water crossings (mostly at night), it can be a bit rough. There was only a single one-day case of seasickness among the divers, but at times the boat would roll hard for several hours while under way. None of this affected the diving, when the boat was anchored in more sheltered locations.
Diving is from zodiacs, in groups of 3 or 4 guests to 1 guide. Divers could stick with the guide, with a buddy, or solo. Divers surfaced with a (required) SMB and were picked up by a zodiac. The guides are expert at spotting and pointing out interesting stuff, so people typically follow them. Divers on these trips tend to be experienced and skillful, but the crew will do EVERYTHING for you if you let them-- carry gear, rinse and hang wetsuits, etc. Almost all divers doff their tanks and fins in the water and let the driver haul the gear into the zodiac. Back at the boat, the crew takes all gear from the zodiac and gets it ready for the next dive. Divers normally wear their tanks to walk (about 10 feet and a short staircase) from the dive deck to the zodiac. But two divers (while expert in the water) could not safely handle the weight, so the crew carried their BCDs and tanks to the zodiac for each dive.