One word, Luko, COST! Labuan Bajo dive centers cater to the backpacker/budget a lot of times. To have speed boats with 2x 250 engines to get there in 45mins would mean 10x more fuel costs and bigger investment in sturdy boats. Even though fuel is subsidized, it'd be impossible to offer a product that costs less than $200 a day with a speed boat option, and that steps into the liveaboard price range.
Drew, I was not speaking about speed boats but probably larger fishing boats, like the ones in Thailand or even Vietnam, some boat where there is a space to store dry items and change clothes, a shady part where it is possible not to sit on the tanks, a sundeck where all the people onboard can at least lie, a ladder where it would be possible to come up with full equipment.
I am not sure some of the dive centres that also sell accoms up to 150USD per night are catering to the backpackers crowd.
Indo fuel is some of the cheapest in Asia, maybe if a daring dive centre entrepreneur could invest into a larger boat, they could probably attract the non backpacker crowd. Labuan Bajo as you know is getting more and more tourism (try to find a room start of august you migt see yourself sleeping on the deck of a boat anchored in the harbor), in this crowd many are not especially the young and cheapskates. I've talked with MANY likeminded people in their 30s/40s I met in Flores who didn't want to go on a liveaboard but wouldn't have complained on more comfort against a higher price, and why not a 3rd dive option on the way out or back... similarly to what is done in Phuket.
For some reason the dive centre I was diving with in LBJ didn't want to hear any of the client needs, even the basics... it seems there is something locally in parts of Indonesia that is stronger than that... call it inertia, or deafness...
I am just wondering why the countries around propose nice day trip boats (I've even been on large safari bangkas in the Phils which were more comfortable than the medium sized pinisi most use in LBJ!!! (I've heard CN dive have a larger and better boat though I haven't seen it).