I have way too many of both of these. It's a struggle to figure out which characters go with which plotline.
I never used to have this issue. When I wrote the first two 2050 books, I knew that the characters were meant to be a part of the story. Partially, because that plotline and its characters came from the same dream sequences; they were paired up from the start.
Now, I have a lot of different characters, and I keep swapping them around into various storylines. I have several different stories, hopefully novel-length, residing in my head. None of them are complete enough for anything more than that, but it's been incredibly frustrating.
Only a couple of those stories have cemented characters who will be the main focus no matter what. The other characters just keep getting moved around, as I come up with a new person or idea.
I haven't had this problem in years, not since high school when I wrote random (poorly done) outlines for miscellaneous characters whenever I was bored.
Academic writing has a tendency to fry my brain; I go for a long amount of time without actually starting a book. Now, I'm finally writing short things again, but I'm out of practice. I think that's part of the issue, alongside the fact that I'm at an indecisive point with my fictional work.