Windows NT originally was CPU independent, but only for Little Endian architectures.
This is no problem for ARM processors since they are bi-endian (as PowerPC).
Source: http://en.wikipedia.org/wiki/Endianness#Bi-endian_hardware
There is nothing in Windows which requires fixed endianness. While all known versions of the OS have been shipped on little-endian machines (except XBox 360, albeit running highly modified version of NT Kernel), there is very little dependency on the endianness for all modules except format parsers and network API. Changing that is a relatively simple undertaking, much simpler than building a new version of kernel, for XBox, for example
That can't be correct, since I remember running Windows NT 4 on a PowerPC system.
PowerPC (except PPC970 aka G5, as I recall) is bi-endian (configurable endianness); so are Alpha and Itanium which also had Windows NT ports.
Alpha is most definitely not a bi-endian architecture; it's little-endian only. PowerPC chips can be either, but the vast, vast majority are big endian.
Incidentally (and speaking of breaking compatibility), MSFT is working on a brand new kernel and operating environment (Midori) which does have ARM as a target. But this is an incubation project with no guaranteed release, though it's a very serious effort.