Hmm! Never tried getting it to work with a mega, but I don't see why it would have trouble.
In general, when the shields have failed--and I sincerely regret that I have had a handful--it has almost always been the USB side. And sadly in many of these cases I have never been able to figure it out (I had one person send me his shield and wound up replacing every component on it with that from a known working shield--and it never did work right!)
So I don't yet have anything encouraging. If I find more free time, I'm pretty sure I can get the leonardo working, and that would be the "right" solution for the modern age--the Leo can handle USB directly and act like a joystick if we reprogram the bootloader, which I *think* will be pretty easy. I'm fairly sure that existing shields will work (although I'm not positive).
Sorry I haven't been working on this--I'm about to move back to England for a few years and work and such has been crazy. I do regret the trouble people have had with this--as always I can only come back with the lame "...but it works for me!" in most cases.
Still, I have a lot of faith in the Leo option, just need a few quiet days to dig back into it. Too many projects, too many draws on my time!