I haven't used the latest invocations of the Microblaze or Nios cores but I did try them both when they were first released.
From my experience, the NIOS core and software package is much, much, easier to set-up and use. I had a system running in a couple of hours with the core, parallel port interface, and multiple internal peripherals. Very easy to get started and well documented.
The microblaze core didn't seem as user friendly but if experience holds I would assume this core is more flexible and faster than the Nios. The software environment doesn't set-up easily and the coregen / invocation method is plagued with bugs that cause bizarre symptoms(typical with the Xilinx software tools). Xilinx has no problem letting you squirm due to buggy implementation software. That's why there are so many third party compilers out there.
A plus with the Microblaze is that they have a hard core (virtexII-pro) which follows a similar interface spec. as the soft core. So if you end-up looking for higher performance, the leap woul be easier in the future.
I would assume that Xilinx has improved thier system with later releases so I think you have the right idea to evaluate both of them.
Similar FPGAs in terms of size and speed are priced similarly in quantity. Xilinx tools seem to produce faster and smaller logic for the designs I've worked on, however.