Having T-Ray as the main villain would make a great movie, you'd have to get rid of the magic angle though. Have the whole conflict that T-Ray may be the real Wade Wilson and that Deadpool killed his family years ago.
Really play with the whole insanity thing.
Of course you'd leave it a bit open ended that T-Ray very well could be lying and just as messed up as Deadpool is. Maybe even more so. You could also have Hellhouse feature in the film where Deadpool gets his jobs.
Other than that plot you could maybe have the whole "Landau, Luckman, and Lake" and messiah angle. Deadpool is hired to protect this Messiah that will bring the world eternal bliss. Deadpool's "great destiny" and all that. Get rid of the alien thing, just have a crazy cult and possible biological weapon and have Deadpool save the world from being mindless drones once he realises what the Messiah will really do. It's just crazy enough to be the plot of a Deadpool film.