I’m working on a book right now where I personally like a certain secondary character more than my MC. The character has her own major subplot and I’m always anxious to get to a point where I can further her story. My critique group has all said that they too believe her story is more interesting to them than the MC’s. It seems that my love for that character and her story has subconsciously made her sections better overall.
I’ve heard that if you’re kept up late writing it chances are you’re reader will be kept up late reading it. This subplot turned out better than the main plot because I personally loved it and worked harder at it. Of course, there’s nothing wrong with liking a plot or character more than the main one and it’s great for suspense when a reader’s waiting for his or her favorite POV, but if no one cares about the MC, there’s a problem. I’m now going back and strengthening the MC and his storyline, putting my heart into his plot as well as the other particular subplot. Look over your stories. Are you also favoring another character enough that they’re upstaging your MC?