R-rated X-Men
R-rated Batman

R-rated Spider-Man
There's certain comics where an R-rating would be appropriate. These include the aforementioned X-Men, Batman, Blade, Punisher, Green Arrow, The Hulk, Black Panther.
There's certain comics that are borderline; those that maybe shouldn't be rated-R, but could certainly border on it. Like Captain America, Green Lantern, and Iron Man.
And there's others that, while they should be made seriously, should stay safely within the realm of PG-13: Fantastic Four, Superman, Wonder Woman, Thor, The Flash, and Spider-Man.
An R-rating is not suitable for everything, and it's not even necessary to have an R-rating to have truly evil villains. The fact that none of the villains so far have been as good as they could have been has much less to do with the PG-13 rating and more to do with the direction they went with it in terms of writing.