"The View Grill" in older south Vallarta. Funky taxi ride to get there. Super views of town and the ocean. Great food, service......not cheap. Good place to take the wife or significant other.
I think the one in Nuevo Vallarta is Fajita Republic. For breakfast the puesto in front of the Fajita Republic is excellent. Ask Grace to make you some heuvos rancheros. Its an off-menu item that's excellent. She is only open from about 0700 until 1500.