I have never been to the Maldives, so can't comment.
I have been to Bali and Bora Bora in the last year.
In Bali, I stayed in the Melia Bali, which is in the main tourist area of Nusa Dua. It is on the beach, but none of the accomodations actually have a view of the ocean (I visited some of the other hotels, and a room with an ocean view is rare). I was traveling with a group, but was able to upgrade to a villa for about $350 per night. It was very luxurious, and even had its own private pool and outdoor shower. The villas have a different class of service from the other rooms in the hotel. They have a private dining room for breakfast, and different menus for dinner and room service. The kitchen for the villas is separate from the main kitchen. They pamper as much as possible with floating flowers in the private pool, your choice of bed linens etc. The villas are close to the beautiful beach. I don't have experience with the diving in that area. I know it is offered, but the diving area that is supposed to be the best is in the far northwest area of the island, and is fairly inaccessable to the Nusa Dua/Denpasar area (car travel would be slow, I don't know about flights.) My regret of the trip is that I didn't hire a car and driver for a couple of days and get out of the tourist area to spend a few nights in the countryside. There are quite a few luxury resorts in the countryside, and the view of the terraced land is spectacular. I did hire a van and driver for 10 hours ($100), but it takes about 2 hours to get out of the tourist area.

From the interests that you stated, I think that you would like Bora Bora better. It is a very small island. Hotel Bora Bora is pretty well established as the most luxurious on the island. The overwater bungalows have a published rate of about $750 per night. A lot of water activities are available, including diving, waverunners, parasailing, helicopter tours, shark feeding and great snorkeling. The island, as well as other islands in French Polynesia are surrounded by Motus (small islands) and reefs that break the waves, so the water inside the reef area is unbelievably calm. The area between the reef and island is generally very shallow, you can almost walk from the island to the reef. This is great for snorkeling. The beauty of the island is difficult to see, except from the air (most all pictures you see are from the air, and there are no good lookout points that you can get to by car). There is a hiking path that ends up at a fairly nice lookout point, that starts across from Club Med. It is unmarked and easy to miss when driving by. I spoke with several experiences divers that were very pleased with their dives.
I have seen Hotel Bora Bora's overwater bungalows on auction at Luxurylink.com. I believe they sold for about half the published rate. Take note of the "seasons" in Bora Bora. I think that January through March is the rainy season. When I was planning my trip, I saw quite a few posts from people that traveled during the rainy season, and confirmed that it indeed does have a lot of rain the first part of the year. BTW don't get big expectations for Bloody Mary's. I didn't get any great reports from other people, and left after waiting 30 minutes for a cocktail and menu, which never came. It's claim to fame seems to lie in the fact that there is little/no competition. When cruise boat(s) come into the island, it gets easily overloaded. I can't see that it would be a problem, given that you get a schedule and plan around it (ie: car rentals will be sold out, etc.) Air service to French Polynesia is very limited. I don't know if you could find a package deal that would save you some money, but would be worth checking out. Any time you request rates/information, I would make it clear that it is your honeymoon. They cater to honeymooners, and have special rates and promotions exclusive to honeymooners.

Best of luck to you. Bob