I suppose anything's possible, but I think if the lines consciously degrade their main dining rooms to drive traffic to the specialty rooms, it would be the classic example of outsmarting yourself. The other possibility is that main room quality could go down because of an excessive diverting of resources to the specialties, but again, I wouldn't put that high on the list of things to worry about.
I think food quality at each level is a conscious choice made by each line based on expected demographics, cost, and logistics. The bigger ships get, the harder it will be to maintain overall top quality.
I wouldn't be surprised to see specialty restaurants at full cost (as opposed to token tip payments) before long. It looks like the train is on the track for more choice in cruising, even on the same ship.