I have that happen to me sometimes! It's also happened with major characters and minor characters in one of my older projects. I wrote some "meanwhile, back at the ranch" scenes to show what was going on with minor characters, and then I realized that they were so much more interesting than my protagonists.

At the moment, I'm rather fond of my "antagonist." It's been a weird journey. The main character will villainize the "antagonist" for most of the book, but then I think they'll end up being awkward allies. :D