Your list includes some of the best diving I have experienced...except for the gilis, great islands to spend time, but the diving was not on par with the rest of them (IMO). If you are in the PI while live aboards are going out to apo reef and tubbataha, I would think you could compare the dives with places like sipadan or the similans. If looking for the muck critters of lembeh, go to anilao, and consider a bit of diving around davao (especially the night dives). For something similar to bunaken, perhaps the walls of balicasag and cabilao would be worth checking out, and gensan has nice wall diving and offshore reefs. I don't know if you get into wrecks, but diving around coron offers good wrecks with macro critters to boot. Southern leyte really impressed me as well, along with apo island. etc...philippines is a great country to travel around and experience the many different dive opportunities.
I could go on, but my point is this... I think if you make the effort to check out the philippines, you should not be disappointed. Many places to dive, with great variety to offer. Best to have a longer bit of time to spend, so you can spend time in several places and find the place that suits you best. If you are limited for time but not concerned about cost, go when the live aboards are going out to coron/apo and tubbataha. Making a honest comparison based on your question means I have to say the diving around indonesia and malaysia is really hard to beat but if you enjoy traveling and diving new places you should be happy in the philippines, its a fun place to spend time.
I could go on, but my point is this... I think if you make the effort to check out the philippines, you should not be disappointed. Many places to dive, with great variety to offer. Best to have a longer bit of time to spend, so you can spend time in several places and find the place that suits you best. If you are limited for time but not concerned about cost, go when the live aboards are going out to coron/apo and tubbataha. Making a honest comparison based on your question means I have to say the diving around indonesia and malaysia is really hard to beat but if you enjoy traveling and diving new places you should be happy in the philippines, its a fun place to spend time.