I was also underwhelmed by Bunaken. I've dived some amazing walls and reefs, and Bunaken is good but doesn't come close to those at Sipadan. I dived Bunaken for 4 days, mostly on the walls, once on a wreck and a couple mandarin dives. The wreck was good, great dive.
On the other hand, I absolutely loved Lembeh, I was completely blown away, having dived some great macro places, Lembeh out-stripped my expectations for critters and it was a photographers heaven. I saw almost all the critters I thought I could bar a blue-ring octopus (not from lack of trying).
If you're looking for resorts, I dived with Two Fish divers in Bunaken, which was fine, guides are good.
Divers Lodge Lembeh were unbelievable. Really great resort, the food was great, accomodation fantastic. Amazing staff, everything we wanted they gave. We asked for 5 dive days, doing an hours bottom time each, then switched to 4 dive days with around 80mins bottom time. Leaving the resort at 7, arriving back at 10. You really do set the schedule. And at the price for the all-inclusive offer it was the cheapest diving I've done. I would definitely return if I'm in the area and have the money.