We dove there in June 2001. Stayed at the Blue Marlin Dive Center. The rooms were clean and comfortable, but nothing to write home about. If I remember correctly, they had AC. The "resorts" on the main strip of the island are pretty close together, so they don't really have a lot of grounds. There was a nice italian guesthouse about 1 mile away from the main town, and it looked pretty nice from the dive boat. Blue Marlin did play pretty loud music until about 10 PM, but when we were there it was the World Cup season, so everyone was in a festive mood with the Korean team making it pretty far!
The highlight of the resort was our divemaster, Anding (aka "dog"). He was knowledgeable and friendly, and very accommodating to our dive needs and preferences. He made diving a lot of fun for us!
I do remember the coral being completely dead above 18-25 meters at most dive sites, due to both previous dynamite fishing and "el nino," which had struck 1 year before. It will probably take many many years for the coral to come back. We did see many turtles, mostly hawksbill, and quite a few white-tip sharks and cuttlefish. The highlight of the trip was the night dive we did at the Meno wall, we got to see a few sleeping turtles, lobsters and an octopus.
The setting of the Gilis is definitely unique though, don't leave without climbing to the top of the hill on Gili Trawangan for the sunset! You look west and see Gunung Agung in Bali (3142m), and look east and find Gunung Rinjani in Lombok (3726m).
Overall, we spent a good, relaxing, laid-back 3 days there. The coral in Bali is probably in better condition and you may get to see more interesting fish and pelagics, but the conditions can be rougher also.
I would advise you to try and dive in both islands, if you can! You can go from the Gilis to Bali in 2.5 hours on the speedboat.
Enjoy your trip!
J.