MacSlash has an analysis of the underlying factors that forced Apple to pull the covers off of Project Marklar.
The long and short of it is that Motorola's business is focused on CPUs for embedded systems (which need low power consumption more than they need more MHz or GFLOPs), and IBM's CPU business is quickly migrating towards game consoles (where Apple's demands are a drop in the bucket, compared to what Nintendo, the XBox and Playstation gobble up).
In the end, if Apple is in the business of building desktops, laptops and servers, it needs a CPU manufacturer that's aligned to those markets. Which leaves two vendors and one platform: x86.
Interestingly, Microsoft's actions to use a 3-core PPC from IBM for the XBox may have accelerated the demise of the Apple/IBM relationship. Surely this will surface soon among the conspiracy-minded Mac faithful, but realistically, it's just an indication that the high tech is a rat's nest of relationships, where everyone is simultaneously your closest partner and fiercest rival.