Yep, I love Cebu but I'm not here for the food. You hit the nail on the head though, you have to work at it to find the good places. You have to judge everything on the Asian scale instead of the European scale (price, service, quality). A few places I like:

In the city: Kaishu Japanese Restaurant. Good sushi and Japanese, kinda out of the way.

In the city: Kiwi Lodge. Nice place to stay and eat both. Cheap rooms compared to the name brand hotels. Run by an Australian.

In the north: Skips Beach Resort. Same deal, stay for a few days and enjoy the beach. Nice kitchen there. This is right near Malapascua but cheaper than the Malapascua resorts. Stay here and make day trips to Malapascua.

In Malapascua: Exotic Dive Resort. Good resort, food and diving operation.

In the south: Marine Village Dive House, Santander (sorry, no URL). They have a great restaurant and scuba diving. They used to be Japanese-owned (I think they still are) so the restaurant is run well. If you are staying the night, do NOT get a "Semi-deluxe" room (across the street in another building), you will be sorry. Spend the extra couple bucks and get the deluxe room.

In the west: Savedra Dive Resort, Moalboal. I honestly don't remember if they have a restaurant, but there are many good ones within walking distance. There's a great pizza place just a few doors down (the one with its own pool).

In Bohol: This one is for divers only. Try to get to Balicasag Island Dive Resort for at least a couple of days. AFAICT, this place is run by the government and the only way to book a package is to call the Dept of Tourism directly. It's weird, but the diving out there is incredible. If you book a package they will pick you up at the ferry terminal (from Cebu) and magically get you to the island. And back again at the end.