Have you ever experienced poor condition bathrooms and bad organization for planning the dives?
The bathrooms are not obviously their forte, but on my side I don't value much the bathroom comfort factor for a dive resort as long as there are western toilets and a shower with hot water. On the other side I agree that it's better to use mineral water for brushing your teeth, the tap water is especially not nice..
As for the dive planning, I can't see how any other operation would do better than them, for me it has always been : say what you want, we'll try to do it. This is were they do excell.
SMART is probably more into creature comfort but it seems their boats are more crowded than BD's. If money were not a problem I would hesitate between Borneo Divers for the dive guides and Sipadan Water Village for the luxury. (In fact I would just return with my Borneo Divers friends

...)
Edit : after you mentioned TripAdvisor I went reading the comments on Borneo Divers to get an opinion, I woudn't care much from the bad reports I read. for example there is one review which is written by a group of italian who I have been diving with for a couple of dives in august this year : If i remember well they're in the group chasing the turtles in one of my photos posted above.
It's a typical example of the wrong persons at the wrong place, Borneo Divers is a dive resort NOT a beach resort, no fancy dress, tea parties or disco nights. On the first days of our stay we were wondering with my wife how they had the idea of staying on Mabul.
I also read some persons complaining that elsewhere than around Sipadan, there was nothing to see underwater (Yeah.. sure there's nothing to spot on Mabul and Kapalai... good joke...) and that if the visibility wasn't good it was the diveguide's fault ?!... Jeeze...