Are the two options for the same amount of days at wdw? If yes, I would do wilderness lodge. The royal rooms are nice, but I prefer the atmosphere and location of the lodge. Plus, for us free dinning doesn't usually fit into how we like to eat and spend our time at wdw. For us it's too many desserts, not enough apps, too many TS meals.
Btw, I'm assuming that you'll be paying OOP for food using the interline discount.