I fully expect Wolverine to be R. They are adapting Old Man Logan, which basically needs to be R anyway. Deadpool just made more money in 4 days than the last Wolverine film (which was really good!) made in it's entire run! That's crazy. I have the R rated version on Blu Ray and it has a scene where he is throwing ninjas into a woodchipper!
The biggest reason why Fox won't think twice about this though, is they do not have the rights to make toys or any merchandise based on the X Men characters. So it wouldn't be a case of a boy playing with his Wolverine figures, but not being able to see the movie. I think Fox will keep the X-Men movies PG, and have a whole other line of R rated films, including X FORCE!! ahhh