Not much difference, honestly. Its a quick and easy walk between the two, as they are connected on floor 3, so no significant advantages in terms of location.
Waimea is slightly smaller so may be a little quieter. Closer to the parking garage, spa, adult pool, and Ulu Café.
Ewa is closer to the store, Makahiki, Olelo Room, Off the Hook, Aunty's, and Ama Ama. Its also is closer to the lawn where the luau is held so some rooms have views of that. Our room in Ewa overlooked the courtyard of the convention space, which was fun for people watching.