This answer is now incorrect - Apple have reverted this decision.
Well, one potential problem with using Itanium is that, according to the new Apple developer agreement, you cannot develop for the iPhone using anything other than C, C++ or Objective C. Specifically you cannot use any third party tool to develop a native application. For more information see these sites for some more details, or google for "apple iphone third party compiler".
Here is a statement from the CEO of Appcelerator about the announcement and what it might mean. Long story short, at the moment no-one seems to know. Definitely out is the old Flash→iPhone compiler from Adobe, but some people believe that there are shades of grey in the middle.