With Vision appearing in AoU you would expect at the very least for him to show up somewhere in the comics. Maybe in one of the Avengers books (Uncanny?) or maybe his own title. With some of the solo's we've had since NOW it wouldn't surprise me.
The Skrulls, much like Wanda and Pietro, can be used by both Marvel and Fox. I remember Feige stating so in an interview a while back. Not sure what the conditions are though. But the dream is alive!