go for dumaguete!!!
ive been there 4 times and i just love it
diving in apo reef is amazing, many big fish and beautiful soft corals.
ive never seen so many frogfish before
dauin is also good and there is also a pier ( iforgot the name) where divers frequent. apparently there are unique coral growths in the wooden beams of this pier ( i havent been there)
aside from diving you can go:
dolhpin watching which includes a buffet lunch trip to a 4km sandbar
the numerous waterfalls - beautiful and near the city
take a walking tour to siliman university
have dinner in many good restos
go caving in bayawan which you rapel down and has an underground waterfall and beautiful stalagmites
go walk along the boardwalk
go white water kayaking ( definitely not for beginners)
canyoning
take a serene boat ride in their twin lakes
take a 1 hr boat ride to siquijor - the old spiritual capital of the philippines with local witches, great scenery, and amazing diving ( so ive heard)
and much more!!!
i consider dumaguete the adventure capital of the philippines. it would make a totally kickass honeymoon imho
atlantis is definitely on the more expensive side id suggest you look elsewhere
pm me if you need some local contacts
cheers
edit: the pier is ducomi pier