I can vouch for Sipadan Water Village.
Was there in 2005, and it was a treat. I didn't get one of their "best" suites, but mine was roomier than I've had before. The top-of-the-line ones had jacuzzi's too.
I can say this about the diving: During our "check out" dive off of the dock we saw an ornate pipe fish, clown fish, several varieties of lionfish, razorfish, Pink & Tomato Anenome fish (often called Clownfish), striped catfish, and several large turtles.
A great sun-down dive from the dock is to see the mandarin fish mating.
Most of the dive trips require that you start suiting up when you leave the dock, or you're not going to be ready when they hit the site. Sipadan is the furthest, about 20 minutes away. Kapalai is about 10 minutes.
One thing i like about the resorts being over the water is you don't have the fly/gnat/mosquito issues. The bugs don't fly that far out.
Anyway, that is the trip I now judge others against. But I warn you, it will be a tough act to follow.
About the only pain is getting there. You go from L.A. to Taiwan, next stop is Kota Kinabalu, then a quick hop to Tawau, where you board a van from the resort to go to Semporna, then on the water ferri to the island of Mabul. Plan a full 24 hours en route. Funny though, once on the boat I was fully awake and ready to go again!
On the way back, I stayed in Kota Kinabalu and visited the oranguatan sanctuary on Borneo. A great way to round out the trip.
Hope that this helps....