I guess you have a point with the face buttons. My bad for not thinking about it, since my experience with dual analog games come from 360 FPS games where you only have to use two analog and the trigger buttons most of the time.
But, still, isn't the 3DS d-pad used to replace or replicate the face buttons functionality with the CPP? I can only think it would be the most logical thing to do.
Of course, they can patch each individual CPP game to support an upgraded revision, but it would bring a lot of problems like the willingness of companies to do so, the requirement to have a wi-fi connection, your 3ds in latest firmware and to manuallly find and download the patch at the eshop which is not that user-friendly experience we all would wish for. The CPP hasn't been exactly a success and I don't think a new revision is likely. But to be fair, the desing presented in the OP is much better than the desing we have now it's a shame they didn't bother to do it like this since the beginning.