I've been browsing for hardware for another robotics project, and thought I'd share some of the stuff I've found.
Have you considered
www.fit-pc.com/web/fit-pc2/ as another option for a CPU? I haven't bought one yet, but it's supposed to be able to run off 12 volts unregulated 8-15 volts, and has an Intel Atom CPU in it. And a wireless card built in. I've also heard that OMAP4 (Arm Cortex-A9, dual core) boards will be coming out within a couple months. I'm rather excited about that last one.
Here's a AVR micro-controller that you hook up via USB, and will give you quite a number of analog and digitals.
www.pjrc.com/teensy/index.html If I'm reading the website correctly, the best part is that their USB interface on the AVR is done "right", rather than just as a USB->Serial adapter.
As a bit of information, it's actually pretty easy to rip the guts out from the bottom of WPILib and replace it with something else. I was able to get joysticks working, and Victors/Jaguars working by just modifying the DS class for the Joysticks, and implement motor controllers similarly easily (I forget how), before I got distracted and moved on to the next project.