Bones, too, is in a different universe - the higher tech imaging devices plus the Jeffersonian Museum instead of the Smithsonian.
I think a crossover between the two would be a lot of fun - and possibly plausible.
Even more fun - we know that the Law and Order universe is the same as the X-Files universe (via John Munch.)
It is all too easy to imagine a situation where a young Goren (who was a profiler for the FBI) meets a young Mulder. They can lack-of-affect at each other prettily. (Note - this is one case where I don't think slash would work. Mulder is quite slashable, but I'm not entirely sure Goren has a sexuality.)