I did my technical wreck penetration course with Sam Collett of Tech Asia, and I recommend him as a good instructor (I am an instructor myself at the recreational level, and I judge based upon fairly high standards).
Technical Diving Courses - Puerto Galera - Philippines He teaches the course in Subic Bay. There are some nice wrecks there and the USS New York is especially fun to dive. There's a little airplane wreck in about 6 or 7 meters depth just outside Vasco's that's great for doing lots of skills practice in tight restrictions and bad viz. El Capitan and LST (Landiing Ship - Tank) are also enjoyable wrecks, and there are a handful of others in Subic that I didn't dive. The New York will be the highlight of any Subic Bay trip, though.
I also recommend Matt Reed of Evolution as an instructor.
Technical Diving with Evolution, Malapascua, The Philippines. He's based in Malapascua. I did a trimix course with him, not a wreck course, but he is a good instructor and I'm sure that that applies to the wreck course as well as trimix. After the course we did some interesting penetrations into the Dona Marilyn ferry, which is where you would do much of the wreck course if you did it on Malapascua. During my trimix course I did a couple of very enjoyable dives on the Mogami Maru (aka the Pioneer) but it doesn't really offer the difficult penetration opportunities that you'd want for a properly-done technical wreck course. So I think you'd be seeing a good bit of the Dona Marilyn, which is a nice wreck.
Based upon my experience, you wouldn't go wrong with either Sam or Matt as an instructor.
I did a liveaboard trip to Tubbataha and had a wonderful time: not great for macro but I didn't complain about that when there were so many fishes (both reef fishes and pelagics), reef sharks and turtles on almost every dive, etc. Search and you can find my trip report from a couple years ago. Malapascua offers a really nice variety of dives, including sharks, wrecks, macro critters, etc. I haven't been to Puerto Galera, Coron, or Apo Reef yet but I'm going to dive all 3 of those in February. Bohol, Apo Island, Anilao and Balicasag are all on the to-do list as well.