Fundamentally expensive. High voltage, low speed, large cache. Old manufacturing process. Not dual core (just multiple die per chip). The current ia64 implementation doesn't seem to lend itself to easy speed increases, given that the top speed is just 1.66ghz, and that after 6 years of development.
I could go on, but really, Itanium isn't an option unless Intel had nothing else, including the Atom. They could ramp the Atom up a lot faster.
In the extremely hypothetical world of x86 mutually assured destruction, where no one can build any x86 variant, I'd expect IBM's power chips to come out on top, at least in the short term. Linux already runs on them, and Apple/Windows has recently run on them. Be a pain to switch, but possible.