For my dissertation I will require the ability to move bones in a charachter through code.
In basic form I will be using the Wii remote to perform basic arm movements and I want to be able to move the on screen charachters arms in the same manner.
It's not for a fast paced action game or anything, its more for a utility type application.
Is this sort of thing possible with JMonkey?
Should be. It's fairly straightforward to read the Wiimote in Java.
You can also load boned models into JME and manipulate them there.
You would have to come up with some sort of method for translating the accelerometer readings into bone rotations, of course, but I assume that's part of the dissertation.
Yes it should be possible. Couple of Wii related threads on this forum as well:
Head-tracking Math, or, Porting Johnny Lee’s WiiDesktopVR C# / DirectX Demo
Wii controller
Should you undertake this project, I hope you will keep us posted with updates 
My mesh.xml library (which will be released soon) will support manual bone control.