There is an analysis of the Intel settlement at AnandTech, which talks about Intel, AMD, NVIDIA and how they may, or may not, be getting along swimmingly henceforth. But buried in the discussion is the fact that support for the PCIe bus by Intel was part of the suit and settlement. In particular, Intel is only committed to support the bus through 2016.
The article goes on at some length about NVIDIA not being on the same page as Intel and AMD; the analysis of PCIe support is only in GPU terms. But not just super duper gamers graphic cards use that connector. Fusion-io, among a growing number of others, does too. There have been changes to "standard" disk drive connections over the years, so in one sense this could be viewed as just business as usual in the computer business. On the other hand, will EMC, IBM, and such be as easily convinced that Fusion-io (or whoever) has gone on the right path to SSD implementation? Knowing that all of your storage protocol could disappear at a known point in the future might give one pause.