Can't help with Liveaboards (although I recall looking at the Hans Christian Anderson). I spent 7 weeks across Jan/Feb/March in the Philippines this year on the recommendations of people on SB. I keep meaning to do a trip report, but in short I had an amazing time and did some fabulous diving.
My itinerary:
* Coron (1 week)
* Malapascua (1 week)
* Moalboal (3 days)
* Bohol (2 weeks): (Panglao - 1 week, Anda - 1 week)
* Subic Bay (didn't dive as I was exhausted)
* Puerto Galera (2 weeks).
The best of all the places I visited was Anda, which is about 2-3 hours along the east of Bohol from Tagbiliran. It's a bit of a honeymoon destination, but I found a great budget room and great diving. It was the closest I came to truly untouched reef, I think. Often there were only 2 or 3 divers in the water and the quality of the dive sites is amazing. Highly recommended. Actually, Bohol was a don't-miss. The top-side activities were great, the culture everywhere was lovely and the diving was the best all-round.
Being a bit of a wreck nut, I loved Coron. That being said, it's a dive-factory and they seemed to put a lot of inexperienced divers inside wrecks with poor visibility and bad torches. On one occasion I had to help a diver from a group of 8 get out of a wreck as she started panicking with claustrophobia. If you can run to it, pay for a private dive guide and try and dive from a smaller boat. I can't speak to Subic as when I got there I really ended up sleeping and relaxing and didn't end up diving.
Malapascua was fabulous. Stayed & dove with Evolution and can't speak highly enough of the quality of the operation. The diving was great and small dive groups the norm. I think we rarely had more than 4 and mostly it was just my friend and I. They also have plenty of dives going out each day, which means if you're minded to sleep in, that's fine, or if you want to do all your diving in the morning, that's okay too.
Moalboal was good, Pescador Island was a great dive site, but I found the diving became a bit repetitive and we dove pescador daily as did everyone else. I also didn't really enjoy the ambiance of Moalboal that much. Perhaps because it was sleepy-season and mid-week, but I was a bit disappointed generally.
Other places I looked at (and would have liked to go): Sogod Bay, Siquijor, Anilao, El Nido.
If you would like any more information, feel free to PM me. I do still have most of my information and all of my dive details, I've just been lax about doing up a trip report. FWIW the trip reports people have posted here and on Thorntree were really very helpful for me in planning my trip. I also asked the same question you did in about November 2011, and got some great advice on timing and stops.
Good luck & have a great trip!