Just got back from KBR.
Here are the way the big three (Lembeh Resort, KBR, and Kasawari) stacked up when I analyzed it: Kasawari is smaller, nicer and significantly (50% when I checked) more expensive, Lembeh Resort is smaller and has alot of stairs to climb (Depending on which room you get), and KBR is larger and no stairs. I didn't analyze SDQ, DLL, or some of the other operations.
Having come back from KBR though, which was really nice, I think the number one most important factor (after your basics, like AC and maybe nitrox and whatever) are met of course) is the dive guide ratio. Much more important than I expected. With too many guests per guide, you end up jostling around, waiting a long time, trying to take a picture of an animal after somebody already silted the area up, getting a fin in the face or (!) on the animal you're trying to take a picture of, etc. Just too many divers in too small of an area, since you need to be pretty much on top of the guide/animal to get a good look at it or photo of it. If you get your own dive guide, it is pure luxury. They can do so much to enhance your experience underwater, especially if you're an obsessive photographer like me. They learn over time what you like and don't like - mine quit showing me 80 different frogfish and scorpionfish after about the second dive once he realized I was a shrimp and seahorse person, not a frogfish/stonefish/devilfish etc person. He can do a better job showing you the creatures without scaring them, of coaxing them gently (they're all very adroit at doing this without bothering the creature) into a good pose, of assisting you with positioning your camera/strobes etc, allowing you to stabilize off of them and their pointer stick, helping you from time to time if you have floaty feet (ahem), alerting you if your strobes act up, telling you if you are forgetting to put your closeup lense on for a very small critter, the list just goes on and on.
KBR has a theoretical policy these days of no more than 4 to 1, with generally two dive guides to a boat. If you're not a photog, that may be fine. But for an obsessed amature photog, I realized that no more than 2 to 1 is acceptable, and even then only if the other person is not a photog or is a casual photog. KBR was very accomodating with the dive guide - over 4 days diving, I had only one unacceptable dive (1 other serious photog and 1 non-photog). The other dives were all 2 to 1 (with me plus a non-photog) and 1 to 1. That happened just by happenstance, logistics, the makeup of the groups who wanted to dive together, etc.
You can make arrangements for 2 to 1 or 1 to 1 for an extra fee at these places - if you are a serious photographer, I would spend the extra money ($80 per day at KBR for 3 dives) for a 1 to 1 ratio, rather than spending the money on a resort with cushier rooms.
May was a good season - resort not too full (KBR had between 8 and 12 guests the days I was there, out of a possible 36 or so), weather just right (hot and sunny, but not tooooo hot), critters out in force.
Also, the location of the resort might be important to you if you like short boat rides and less hurried surface intervals. KBR, Lembeh Resort and Kasawari are located pretty centrally. Divers Lodge Lembeh is way down on the southern tip of Lembeh Island, perhaps (I've never been there) requiring multi tank dives or long boat rides.
I would dive at KBR again, but if LR or Kasawari gave me a better guide ratio at a reasonable cost, I'd go there instead.
As Lynn said though, the diving and camera facilities at KBR were excellent. If you go, get the multi room cottages, and ask for the ones between the dining hall and the dive shop. Best location to minimize walking time.
To react to Alan's post, I'd say that I definitely needed the a/c at KBR. There was a breeze, but it was only nice if you were out on the dock, in the briefing huts, and on the balcony of the restaurant. Too hot in the room without a/c, even at night.
As far as time limits, KBR was enforcing a 60 minute dive limit. I was using up my air in that amount of time though, so it didn't bother me much. YMMV.
Hope that helps! Lembeh was great.
Taxgeek