I modified my trip quite a bit once I was there. I think the thing people don't realize before going there is that travel between places will take 1 whole day. There's no way to make it less - it takes a whole day. So that limited the number of places I went to.
I spent 11 days at Peter's Dive Resort in Leyte - diving there was amazing and I didn't want to leave. Beautiful reefs. They're recovering from a crown of thorns attack a few years ago at some sites but there was so much hard and soft coral there in great condition it's hard not to love it. Small amount of macro stuff too. Then I headed by overnight ferry to Cebu (not very comfortable, but cheap) and went to Panglao/Balicasag/Pamilacan (Valm Dive) - I wouldn't recommend that actually. Snake Island was cool (though with the current, only 20 min dive), and some of the diving was nice - but the reef and the tourists there made me a bit sad. Damaged reef, tons of Asian tourists not respecting the reef and other divers' personal space.
I went there because getting to Malapascua was going to take forever and the diving in Leyte was so good I figured I could miss the thresher sharks and save an extra day or two traveling. Also travelers I met said Malapascua was ok, perhaps not worth the long trip there if you're already going far to Leyte.
From Panglao I went to Dauin/Dumaguete (Dumaguete Divers) which was very interesting in terms of macro life. Also Apo Island was very pretty with some nice big fish. I wasn't in Dauin proper, so maybe the diving is different, but there was a lot of good macro stuff in Dumaguete.
After a few days there I went to Anilao which was unbelievable. There's life everywhere you look. And a ton of macro stuff too - more than Dauin, though I saw some unique things in Dauin that I did not see in Anilao. If you're looking for macro goodness, I'd go to Anilao, though everything is more expensive there. I stayed with Buceo Anilao. There was some reef there too, and life aside from macro, but I seemed to be the only one who would put his camera away for 10 minutes and explore the non-macro world. If I had to rank them, and this is by no means a contest, Leyte > Anilao > Dumaguete > Panglao. Regardless, there's a lot out there for everyone.
Summary:
S. Leyte - 11 days
Panglao - 3 days
Dumaguete - 3 days
Anilao - 5 days
There's still a lot more to see, including Coron, for my next trip. Apparently it's better if you've got your nitrox certification because the wrecks are deep. Remember that travel between places takes a full day typically. Hope that helps