I have no experience on software side, hence, hard to tell if there will be any advantage/hurdle for switching from PowerPC to x86 at instruction level. However, I'm kind of wondering that the reason for Apple to jump to the Intel/x86 bandwagon is because the volume of Apple boxes/systems won't be attractive/huge enough for sustaining IBM to customize their Power/PowerPC-based silicons for desktop systems. While Sony, Microsoft, and Nintendo all debut/announce/plan their next-generation game consoles with more powerful PowerPC (either 1 or 3- PowerPC 970-class cores inside) core(s) inside (at least, Apple doesn't have PowerPC 970 running at higher than 3GHz frequency), Apple is awfully left behind as its flagship G5 system will look not that great compared to those game consoles (say 2.4GHz G5 system from Apple with one PowerPC 970 inside compared to 3 x PowerPC 970 @ 3.2GHz cores inside XBox 360 Xenon processor). Unlike Sony, Microsoft, and Nintendo, Apple doesn't pay extra money for customized processors (IBM is moving into more design service instead of selling the standard parts like PowerPC 970 chips), therefore, I suspect that from IBM perspective it may not be lucrative enough to focus on Apple account compared to other customers.
If Apple continues hanging with PowerPC architecture, Microsoft can easily step into Apple's turf by enabling Windows running on XBox 360 and re-brand/sell the three-core inside XBox box as Super G5 system (while you may only need to pay less than a Mac Mini price to get XBox 360 with three 64-bit PowerPC 970-class cores inside).
In a nutshell, I think IBM dumps Apple somehow (as IBM's resource is sucking into developing customized chips for others but not Apple).
Steve Jobs may make a right choice for the time being, but in long run, could Apple be as influential to Intel chip architecture as it used to be to PowerPC chip architecture before? I don't think so ...