Hi Susie,
I have been browsing this site for awhile but as you can see this is my first post.
I wanted to address the cost issue of going to Wakatobi as mentioned by ssra30. There were a few great dive spots mentioned that were noted as being less expensive. I have been to Komodo and the diving is mind blowing. Great critter diving, lush reefs and opportunities for pelagic encounters such as schooling mantas, etc. Komodo is only diveable by liveaboard and to book a 10 day trip the cost would be anywhere around $3-4k for the boat portion. Then add in flights to Bali or Kupang, etc...
I can't tell you much about Alor, but believe it is also by liveaboard.
Irian Jaya or more specifically Raja Empat is now the big buzz and is supposed to be mind blowing as well, with perhaps similar pelagic encounters as Komodo along with more schooling fish, lush corals, tons of critters and inverts and great diversity. It has been very high on my list along with Wakatobi. You can generally do it by liveaboard or a package w/ Papua Diving. Again a 10 night liveaboard is about 300/night and the land based packages are by the week, with 20 dives, so you would book a 2 week trip to get the same amount of diving as a 10 day liveaboard. The cost for the least expensive accomodations is up around $2500-3000 for 2 weeks, plus you have to add in a flight to Sorong, bringing the costs before air to SE Asia to around $3500.
Manado/Lembeh offer some specials for 10 day trips and with air from the US may cost about what the 10 day land package only to Wakatobi may cost, but you really only get just over half as much diving as you would do at Wakatobi for the same amount of time. Lembeh is legendary for it's critter/muck diving and Bunaken has amazing walls and reefs. Likewise, Sipadan has great wall dives and schooling barracuda/jacks/bumphead parrotfish and tons of turtles and Mabul has a lot of the muck critters you would find in Lembeh. I have been to Sipadan in '95 and '99 and can say the diving was excellent, but have seen some of the changes which prompted them to recently close down the land based resorts to give the island a break. You will still love the diving there as it is still awesome, but I am glad they are looking more to conservation to keep it amazing! I think the cost of a 10 day trip to Sipadan/Mabul is around $3300-3500 w/ air from the US.
So here is the comparison. Wakatobi advertizes their 10 day package in a garden bungalow for $2640. This cost includes a flight to the resort from Bali. It includes 10 days of 3 boat dives and unlimited beach diving on what is considered the best house reef on the planet. The reefs are known as being extremely healthy with a lot of great critters and small fish. It may not be as well known for common encounters with pelagics, but if you are looking for great reef diving I hear it can't be beat. The overall cost w/ air from LA is around 3300-3500 or about what it would cost to do the same length of a trip to Sipada/Mabul or just a little more than Manado/Lembeh, but with a LOT more diving. It is also less expensive than the trips to Raja Empat or on many of the Liveaboards in Indonesia, taking all of the travel costs into consideration.
Given all of the above and having to narrow my choice between Raja Empats, Manado/Lembeh and Wakatobi, I found Wakatobi was a better deal for that level of great diving with the amount and freedom of diving I wanted to do.
Given all of that I just booked a trip to Wakatobi for November, and can't wait! Of course I'm sure there are people who could comment more on what to choose based on having been to more of the places, but I could only respond with what I have found looking into the cost issues for similar levels of service and diving and can say Wakatobi doesn't sound like too bad of a deal, from what I've found!
Enjoy your trip to Sipadan/Mabul...I'm sure you will absolutely love it!!!