This reminds me that a couple of years ago, between C2 and C3, CR had it's own mini-controversy when it updated it's Fan Content policy to better protect their own IP (including, among other thing, reserving the right to use Fan Content for their own purposes without compensation to the original artists).
I suspect now that they will have to make the same choice that many others are making, looking at the cost/benefit of staying linked to D&D vs going their own way. Since many of the same potential issues would exist if they went with another publisher's game as it would staying with D&D, if they decided to break from D&D I would guess it would be to use their own system.
What I hope is that CR (or anyone who decides to stay with D&D) doesn't get hate-flamed for the decision.