I think that really depends on your viewpoint. You're right that the tonal differences will be subtle, however such subtleties are what makes certain recordings sound the way they do. Imagine if Jimmy Page had never used his pickups out of phase...that's not a standard pickup configuration for most players. I do agree that the name "Game Changer" is a bit arrogant and may be an overstatement, but the idea behind it is the same as the Axe-Fx. You get a zillion options for your tone without having to own a zillion different guitars. And you don't have to break out the soldering iron every time you want to add a coil split option, invert phase, or try some crazy pickup configuration.
Personally, I see it more as a time saving tool than a real game changing innovation. I can focus more on playing the damn guitar while still trying out new settings. Axe-Fx Ultra + Game Changer = Eleventy-Zillion tonal options with one guitar and one 2U magic black box.