3 musts (imho)
1. Skully AND mulder need to be part of the fbi.
I don't care how or what contrived way they acheive this but the whole point of the x-files is 'FBI' unsoved crimes.
2. steer clear of alien conspiracies.
there just isn't time to do it justice in a two hour movie, so don't even try.
3. make it accesable to a wide audience.
look at the star trek reboot, you didn't need to know anything about star trek other than the iconic characters. any one should be able to watch an x-file movie with the only knowledge needed is who mulder and skully are.
so with that in mind imagine the following
it's x-files year four (or anytime that places them BOTH in the fbi basement) so both mulder and skully are very much part of the x-files (they'll look older than they did, but anyway) they are called into to investigate brutal murders commited by people who were up until the crimes were normal law adding citizens.
they find out using investigation and mulder's out there theories that this is being caused by a being that is able to control peoples bodies go on a killing spree and then leave the host when the body is too damaged. when the being is finally revealed in all it's glory its a kick arse monster.
* investigative police work.
* kick ass action scenes.
* special effects.
so frigging easy and general audience need no NOTHING of the x-files methology
who did the last movie appeal to? the fans? no, I'm a fan and hated it. the general audience? no, because I bet they didn't know what the heck was going on.