You're definitely right, Wakatobi Dive Resort does provide luxury for a competitive selling point for those who can afford it. I have been around for 6 years and still haven't step foot on their private island but believe me i wish
Now you're asking me a tough question and asking me to compare to very specific spots. I would say that Bali, Raja, Komodo, Wakatobi have definitely different kid of diving and different vibe.
Why would i go to Wakatobi ? It's remote, there is literally nobody there. In six years diving i have once saw other diver in the water. There is so few people that we just change site if we see one of the very very few diving boat. The coral is pristine, lot of variety and very healthy. The scenario of deep walls is dramatically amazing ( i am a big fan of wall dives). The arquipelago is empty of tourist, and that is a special experience on my opinion. Cherry on the cake , there are some cenotes available for cavern tour.
I am trying to be objective and not overwhelmed by my love of the area that made me move there. Creatures like, as someone said earlier in the post, there are less big fish that in Raja and komodo, we do spot very frequently reef sharks, napoleon, eagle rays. Now that i am starting to explore the greater depth i am kindof suspecting that the big boys are hiding past 60 meters under the thermocline. I have seen some big stuff there but this is still under investigation.
Topside options are mostly gonna be about nature and landscape but diving is definitely the main attraction around here.
As for pricing, you have several accommodations options available in the main island (Wangi-wangi) ranging from 10 usd a night to 60+ . Most of them are not available online but i can assist on booking if needed. Food is as usual in indo, very cheap. Note that they are mostly not any western food restaurant on the arquipelago so you will have to go local

I would say that the value for money is ok, diving may be a tad more expensive than shore dive in Bali due to remoteness and rising price of gas. Our DC organize diving around Wangi wangi where there is a lot of dive sites. We also have popular seafaris where we would go all around the arquipelago with our boat and sleep on land. The more you are the less its expensive as the extra gas costs will be divided by the number of divers.
Eventually i would say that Wakatobi has the potential of being amongst the big names of dive destination in Indonesia when it comes to value for money and quality of diving. It just lacks easier access and better promotion from local government.
Hope i answered your questions, feel free to ask more if you need to !