Apple seemed to overcome the switch from PPC to x86 CPUs fairly well, so I can't see it being the biggest problem ever. A lot fo software is cross compiled for the 2 platforms, especially in the Linux world.

Obviously the biggest issue is optimising the code to make it x86 specific to take full advantage of the CPUs.

The only other main alternative is to move to a different RISC CPU, which wouldn't require as many changes to the code, and for that ARM is the logical choice, but you would still be stuck with proprietary hardware again which is always more expensive.