Not long ago I read a review of Naomi Alderman's novel The Power, which talked about something called The Minnie Effect:
The Minnie Effect, named for the eponymous character in Kathryn Stockett's The Help, is a phenomenon in POV novels where the best or most entertaining characters are given the least amount of attention within the overall novel whilst the least entertaining or boring characters dominate the narrative.
I've talked about this kind of thing in Disney movies, and also some of their derivatives (see my review of Rock & Rule). It's a weird issue that I've had my own struggles with over time, and I've identified what I think are a few reasons why it happens.
Most stories that are driven by a high concept of some kind don't like to slow down too much for characterization. They're all about providing a showcase for The Idea, and in the mind of the author, stopping to smell any other roses along the way would just be a distraction. Consequently, any protagonist that gets front-and-centered in such a story is one-dimensional by design. They're a tour guide, not a personality. Sometimes you can use this to enjoyable effect — Vampire Hunter D does this all the time, for instance — but if you're not conscious of it, it'll just become tiring.
Disney, again. A Disney movie, and anything roughly in its mold, tends to have a fairly bland character at the center for the sake of the broadest possible audience identification. Disney and its imitators seem to be drifting away from this model, thank goodness, but it's still too easy to fall into.
This is one I have wrestled with most directly.
An author can put a character front and center not because they are interesting, but because the author identifies with them in a way that ultimately means more to him than it does to the audience. Freshman authors get tripped up by this a lot, but it's not exclusive to them.
It almost always stems from the author not being conscious of their motives for picking that character. Nothing is wrong with choosing a character because they have some undefinable je ne sais quois about them that sets the heartstrings a-thrum; just don't get stuck on that alone.
Characters, especially main characters, are supposed to be agents of change, both within and without. With an author-attached character, the author sees far more in the mere existence or presence of that person than they do in terms of what they can accomplish or become. They might still accomplish or become things, but the whole way they do so is compromised. Think of all the fantasy stories out there with jerk protagonists, the Hero-By-Default as I call it. (cough, Sword of Truth, cough)
Note that I'm not talking about antiheroes. This is closer to counterheroes or nonheroes — people purportedly offered to us as heroes, but whose behavior puts the lie to the label.
The book I'm currently outlining suffered for a while from this problem. At the center of it was a character who seemed too callow and limited to be worth following. Then I realized: the fact that he's callow and limited need to be your points of entry. Start off with him in that vein, I told myself, but goad him to level up, to discover himself as an active participant in things instead of just a reactive, passive vessel for them. We're still nowhere near the level of fleshing-out I'd like — I suspect that has to wait until we're in the trenches — but at least I'm not stuck anymore in this particular dramatic glue trap.
My ultimate point: Always be conscious of what the appeal of your protagonists is to you, and how that might not translate into what the reader sees. Confront that, and you may well have a different, and better, story in the offing.