The water bungalows will be a good experience although they cost more. What is important is chosing the kind of resorts that allows you to bath in the open privately !!! i ASSURE you it is a very nice and wonderful experience.
Actually it doesn't matter on whether you are staying in the north or south atolls, if you intend to go to the best diving sites, your hotel operator will connect you up.
Try the subs at male too... nice experience, it'll take you deeper than you can physically.
If you are into fishing, go catch some marlin...expensive though...
Check the season....there will be manta rays migration and all which is breathtaking...
If your lugguage is light, bring some mineral bottled water on your own (you will thank me, 3-4 bottles per person) if you are not a beer fan.
If you can get those small thermos type flask (small ones) you can also bring some specimens home....try the hermits, they are everywhere.
If you love nature, try South Africa too....especially with the rand moving downwards, your S$ will yield more (you gotta hurry though)