I have been to both and personally I prefer Komodo over Phuket for a few reasons. While the Similan/Richeliue are a very nice spot for diving, they have become so congested, too many cattle boats for my taste. I still go there but it seems that every time I go, I seemed to enjoy it less but for me, it is an easy location to get to since I live in Thailand. However, in comparison to Komodo, it has a few advantages, water is quite a bit warmer, generally 28-30C where as Komodo was 21-26C (last August when I was there), the dive is much easier as Komodo has much stronger current and is infamously known for down current but your DM should be able to plan the divesite regarding to current etc appropriately but still, diving there is more challenging but not dangerously so. Andaman sea in season has relatively decently chance of seeing whalesharks. I am not sure if there was any report of whaleshark in Komodo however you may have a chance to see sunfish in Bali.
Macro life in Komodo is much better than Similan/Richeliue but south Andaman sea (Phi Phi, Hin Daeng, Hin Muang) is not bad either.
When I was in Komodo, there were total of 3 liveaboards that I saw the entire time so it was ont crowded at all.
Mermaid II looks like a nice boat but I have never been on it.
If everything go as planned, I will be on Aqua One with a couple of other friend in Komodo in early August. Some live aboard will start the trip in Bali and go to Komodo but I think it is a bit of a waste as it takes almost 2 days to get to Komodo by boat and the divesites in between are not all that good. With Aqua One, I will fly to Bali then take local flight to Bima and commute over land to Sape (I think that is the name) to get on the boat then plan to stop for a few days in Bali on the way back to see if I can find the sunfish there.
