I can show you something:

I am actually building hardware for my virtual plugin.
I intend to make it as DIY project - as I have choosen mostly through hole components and easy to assembly SMD components. It also uses FTDI, either as SMD or DigiKey module - so everybody will be able to prepare it himself ( PCB is single layer board, you will be able even to make it on universla board).
Right now it works as standalone device ( not yet from Mach, only from my test app - Mach will be next). I plan publish Eagle design and to sell plugin licenses for the software.
With XMega you should be able to make something similiar ( although it is slightly less powerfull then the dsPIC - I have choosen one of most powerfull CPUs found in DIP package). The critical parameters are the CPU speed and RAM size. 16kB is minimum I would say.
In mach SDK you have examples of sending USB data. Just that you need target device which processes it properly.
Timers are not that easy to be used as pulse engine - you would need at least four independent 32 bit timers with configurable pin control, otherwise you may have resolution problems to operate with e.g. 100kHz pulse frequency. Most designs (like SmoothStepper) use specialized cascaded high frequency timers in FPGA