+1 for El Galleon.
I was certified there about 3 years ago, and been back a few times since. Their dive staff is fantastic, resort staff is great, food is good, and rooms are nice. Just be aware that the Sea View rooms are up a few flights of stairs (but awesome rooms).
I agree that Atlantis is over priced for Puerto Galera. Even their dive rates are high.
But Angelyn's might be a good option. It is immediately next door to Atlantis. I have stayed there the last few times (EG was fully booked). Great Price to Room value, and their dive staff is good. It is also right in Sabang, very close to all of the night life and restaurants.
Wherever you decide to stay, be sure to grab a dinner (or two) at Tamarind, located right next to Atlantis. Fantastic ribs, burgers, steaks.... heck, their whole menu is awesome.