I've been to Raja Ampat, Komodo, Lembeh, Tubbataha, Puerto Galera, and Thailand on your list.
For the price per tank and all-in with food, beverage, and lodging considering the dive quality and convenience, Puerto Galera is quite good. Out of that entire list, Philippines has the least expensive diving on a per tank basis. You won't get pelagics in Puerto Galera (not a single eshark all week for us, which I hear is normal) but mostly macro and reef scenes. Verde Island is incredible. You come back between dives and it can be like liveaboard diving that is resort based. Do as many or as few dives as you want but 6 nights, including round trip private transfers from Manila airport, nitrox, ocean view room, all meals, 4 dives per day was $1200 with El Galleon and Asia Divers. It is excellent value and I would return.
Tubbataha is very good and very healthy. It has great whale shark opportunities but if we are comparing it to Komodo and Raja Ampat, I don't think it is as good, whale sharks aside. I love that you get to see them in their natural habitat without feeding. The color, density, and variety of corals (hard and soft) as well as fish and sharks, general life, etc. in Indonesia cannot be beat, especially at Raja.
Lembeh is great for muck. Many people either love it or hate it. I noticed folks tend to like it if they are into the weird and the wonderful or have a tendency to like to spend time looking for small critters. Patience is needed, obviously. Usually, photographers really enjoy going there. NAD Lembeh is an excellent resort. I highly recommend.
I haven't been to the Similans but will head there in late March. I've dived in Thailand before and it is underwhelming compared to the others I have mentioned. In the meantime, I have been to Komodo and Raja Ampat once each already and have plans to return to both next year, October and April, respectively. I will also be checking out Banda Sea for their crossing but that report won't be out until late October 2019.
If you are doing a tour of Asia, I would be strategic about which order you dive it in so that you can appreciate the destinations. You may be disappointed with some destinations otherwise. My suggestion is to leave Raja Ampat for last and Komodo right before that. The two have been my gold standard ever since diving there. There are many liveaboard options for both. Komodo can also be done by day trips though not as convenient. Raja Ampat can be done by land but you won't get to all the different dive sites so I recommend a liveaboard to see south, central, and north.
Let me know if you have any questions. I did a review on a Tubbataha here: liveaboard
Discovery Fleet MV Discovery Palawan Tubbataha Trip Report, April 19-April 25, 2018 Remember the season is late March to early or mid June. I suggest going in late april or early May for best conditions.
Check out the photos I have
www.instagram.com/outofofficebrb
To summarize, if I had to pick one country to dive for the rest of my life..It would be Indonesia.