Hi Shanker,
I myself have several of the MultiWii controllers in Vermont, and I believe the team at EPFL does as well, but I know they have also looked into replacement boards. Right now I do not know the best option if you cannot obtain a MultiWii, but perhaps someone from EPFL can chime in.
What I do know is that researchers in Gusz Eiben's lab in Amsterdam, as well as some former project students of mine, have both used a Raspberry Pi to control the RoboGen, but this required using a larger core component capable of fitting the Pi, and also required modifying the code to run there (but provides many advantages as well).
I know others have used other Arduino compatible boards as well, but I am not sure of the details right now.