From your list, I’ve done Raja by liveaboard and Egypt’s Red Sea by liveaboard and land based. I’d rate PG diving after Indo’s Raja and Komodo but maybe a little bit ahead of the Red Sea. As
@Trailboss123 mentioned, I stayed at El Galleon and dived with Asia Divers. Their house reef is excellent, my favorite being Fantasy Reef. It was great to be able to fit in as many as 5 dives a day if you’d like with them coming back between each dive. It’s a short ride to each dive site with the exception of Verde Island. It’s worth the surcharge and extra time.
I’ve dived Lembeh and PG has some pretty good macro while being able to enjoy some really great wide angle scenes on the same dive. Lots of frogfish, nudis, shrimp, crab but not as varied and weird/wonderful as Lembeh which is way more specialty. PG is great if you’re like me and love reef wide angle, appreciate macro (I’m a photographer) and happen to have divers that don’t care for macro. There’s a little of everything to please everyone. PG diving is not as good as Tubbataha in my opinion, so I’d do that if you could only pick one. For the price, PG is the better value for a week all-in. One thing to note is that I didn’t see a single shark in PG all week and I was told that is normal.
Please let me know if you have any specific Q’s. I just got back from the Red Sea (45 dives....4 days land based and 2 weeks on a liveaboard
...so the comparison to the Red Sea is still quite fresh!
Edited to add: I’m addicted to liveaboards and diving with El Galleon/Asia Divers full board felt like a liveaboard on land. The food there is surprisingly very good and dive setup and center is very convenient.