In June I stayed at Tepanee Resort for 2 nights, thought it was great. Eco resort (by Phils standards anyway) feel to it and nice Italian restaurant attached. They have a very small secluded beach a short walk down the steep hill from the accommodation units. It's tucked away a bit from all the other resorts main beach area but they are only 5-10 min walk away, I thought it was really good value and the staff were great, fond memories of massages under the stars. I would go back to them again. Then spent 2 nights at the Hippocampus which is basic but nice enough and located in the heart of resorts and restaurants part of the island, and right on a nice beach. Staff were just ok, I was low on cash (no atm on island) so made very clear before checking in I could only pay by visa which they said was fine, upon checkout their visa machine was not working. The manager turned on me at this point insisting that I pay cash, by this point I had not nearly enough cash to pay, manager was borderline aggressive, in the end I suggested a staff member come with me to the mainland where I'd withdraw cash and pay which worked fine but I didn't like being made to feel like I'd done something wrong.
I did the thresher dives with evolution divers and it was awesome. They charged a bit more but avoided the crowd, felt they were good.
4 nights was plenty of time on Malapascua for us. I could understand people enjoying it for a week or more but for me and my girlfriend at the time (non-diver) it was a bit too quiet.