Atlantis is a good distance away from the town so it is nice and quiet. We stayed at El Dorado just a short walk away from Atlantis. At night, it is very quiet and very dark around there.
The beach is so so, dark sand but not very crowded. Atlantis has a very nice facility so I am sure you will have a good time there.
Depending on what you like, my friends and I are into photography and prefer macro over wide angle so we find Atlantis and El Dorado housereef the most enjoyable for us. Duine looks really boring but we found blue ring octopus there. Masaplod is also worth a visit, large school of fish, sevearl cuttlefish and octopus.
Apo Island is nice but I was a bit disappointed, after hearing all the good things about it, may be I had too much expectation.