@mdg33
Improvements will have to be made to the RetroArch cores before RetroPie can become a truly viable solution to light gun gaming. The groundwork has been laid for mouse compatibility with lr-nestopia, lr-genesis-plus-gx, lr-snes9x-next and lr-mame2003, but really only mame2k3 is a fully working solution, due to the recent addition of absolute pointer coordinates. Besides lr-nestopia, the rest don't even recognize a mouse of any kind on the Pi like they do on x86 hardware.
Fortunately, as with anything else of this sort, there will come a day when a developer will find this sort of thing important to them and the whole thing will get ironed out. For example, look at the newest improvements to RetroAchievements in RetroArch. It languished as a half-implemented feature for some time and once the interest was found, it it got finished. You can bet that one day in the future, some developer is gonna want to break out their gun and play the NES 'Duck Hunt' or SegaCD's 'Snatcher' on their Pi and the final nuts and bolts will be added.