Hi mstanley
We picked SMART's Water Bungalow at the end. Just got back last week and had the most amazing time there! The over-water bungalows are very comfortable and clean, almost luxurious! The service in general was good as well, friendly staff. The food was OK, there were 2 meat dishes, 1 seafood, and 2 veggie dishes to choose from each day. It got kind of boring after a while as there's so much chinese/malay food you can eat.
Now, the diving. Everything you read on this site about the friendly dive masters/deck hand is true. I felt so spoiled as they moved my gear (even mask and fins) to the boat for us each day. The deck hand was my best friend for sure as after each dive I would take my BC off BEFORE I even got on the boat. The deck hand would appear from the top and yanked the whole thing out of the water for me. Talk about good service eh!
On each dive there were 6 to 8 of us. The boat captain came with us on all dives as well as the dive master, and they are pretty good at pointing stuff out (especially the hard-to-see stuff about Mabul).
We went to the SMART resort on the island and had a look around. It's not as luxurious as the Water Bungalows but the plot is bigger and it has a swimming pool, beach, jacuzzi etc. The atmosphere is more like a holiday camp, like the long tables in the restaurant whereas the Water Bungalows is more romantic and quieter.
I am not sure if booking last minute would be cheaper. With the permit issue perhaps it's best to book ahead, especially during high season. The time we went was considered low season and yet some places were full.