There are still a number of unknown factors.
There's no guarantee yet that IBM is working with Nintendo for the next generation. That was never announced. The GameCube uses a modified G3, but if Nintendo wanted to stay with the same processor family, they could use a Motorola PPC for the next system.
The IBM-MS announcement was vague. For all we know from the press releases, IBM may be manufacturing some kind of CPU, but not R&Ding them. For example, ATI is licensing graphics for the Xbox2, but they're not actually manufacturing the graphic chips.
The PS3 will have IBM's "cell" which we know IBM did R&D. So, still, IBM is double-dipping at the very least in some way.