I don't think that'd be too much of an issue. After all, Darth Vader was the villain for two-and-a-half Star Wars movies and they were still wildly popular. Likewise with the Harry Potter movies, where Voldemort has been the villain in one form or another for about six movies. Audiences have proven a willingness to see the same villain over and over again so long as the stories are good and the villain is compelling.
I think that, if done right, the audience would love to have that "Oh, @#$%!" moment when the villain which they think was previously defeated in an Avengers movie turns up as the villain in a Guardians of the Galaxy movie. I know I had that feeling when I was reading Annihilation: Conquest and Ultron turned out to be the villain behind it all. Sure, something like that would get played out if it was done every time, but I doubt it'd be every time, or even most of the time.
And remember, we're not just talking about reusing villains. Ronan may be a villain in an Avengers film, but that doesn't mean he'd be one in a GotG film. He could instead turn out to be an ally or somebody they have to deal with. Likewise, retaining Adam Warlock's history with the Asgardians is a nice touch which serves as a reminder of the connection without detracting from the overall stories.