According to Movie Pilot on Friday, though this is purely speculative, with the rescue of Wolverine by Mystique in "X-Men: Days of Future Past", one may wonder that her motivation to do so was due in part to preserve mutant kind. That being said, since William Stryker had access to Wolverine and had given upon him new Adamantium claws, it seems that the "X-Men" sequel may have suggested that Mystique's interference in the timeline by rescuing Logan removed the possibility of him of ever being experimented on by Stryker. The same may go for Deadpool.
This also may mean that Deadpool, who was played by Ryan Reynolds in "X-Men Origins: Wolverine", may not have even taken part in the Weapon XI project. Apparently, Stryker saw Logan as being obsolete and unveiled to him Deadpool, but ironically wound up being the "Merc without a Mouth" in the Marvel Cinematic Universe. That all being said, one could speculate the time line change after Logan's involvement in influencing this new one could reveal a rather more "faithful" "Deadpool" movie.
In an interview, "X-Men: Days of Future Past" producer Lauren Shuler-Donner teased at the possibility of a "Deadpool" movie. There's been debate about about doing such a project considering it would be of a lower budget and the ability to "swing" a R-rating for the flick.
Shuler-Donner did mention her involvement with that film and that they are "getting there" as far as as it being green lit. She also mentioned that Reynolds is still attached the movie and couldn't picture in her head that anyone else could play the role of Deadpool either. Shuler-Donner also mentioned that her and Bryan Singer never got to preview the first "X-Men" movie and didn't really think any movie goers would go in droves to see it.
Singer's "X-Men: Days of Future Past" has been playing in theaters everywhere and had made over $500 million globally in theaters.