I was thinking on the lines on why there wasn't any rush for arduino compatible Atxmega series of boards like Atxmega128a3u?(Is it due to Arduino Due?)
Don't know. Other than the maximum voltage, that ATxmega128A3U is certainly nice.
You will need to program a new processor. According to the datasheet you have two choices: PDI or JTAG. Do you have a PDI / JTAG programmer?
Are you planning to develop the hardware and software?
Do you have a specific application in mind?
Will all the things work (All libraries) as with say a normal MEGA board?
I'm going to go with "no". The basic hardware appears to be significantly different (and more feature-rich).