@PGSmobile: I can't imagine how you are planning to make it through a 1351 mouse emulation, since that deals only with some relative movements via SID registers, and will never see the positions. You won't be able to navigate it to any direct X/Y coordinates. It depends on the user application how it reads and calibrates those movements.
The lightpen however is almost exactly the same direct pointing device as the touch screen. It can even be much easier programmed on the user application side (just set up an IRQ and read it).
Another disadvantage of the mousing is that it requires some sprites on screen (whereas lightpen not).
Perhaps a nice compromise could be to have a "hypermouse" which should be a USB mouse (or a USB keyboard at the numpad cursor keys) transparently controlled by the FPGA hypervisor in the background and visible independently of the VIC screen (likewise the onscreen keys), but not recognized by the user program until any left/right clicks are done (which are translated to lightpen events, too). The WinVICE emulator makes it also in this way, so thus you might run a C64 program in a window "shell" as if it were a native Windows application seemingly (controlled from the "outside").