DiGi threw off a remark:

I’ve not recently watched anything specific in the way of anime where the main character has found themselves somewhat usurped in terms of position, though I’m sure such things exist.

Do they? Haibane Renmei contains a masterful misdirection in this regard and I very much enjoy telling neophytes that Reki is actually the main character. Some of them continue to disagree until the last episode, and then have an epiphany. But that's different, because it's fully premeditated by ABe. So, what about the usurption?

In some cases, fans have just enough material to form such view. I met several people that maintained that the whole DBZ is about Vegeta (Fajita), and everyone else — even Gohan and Goku — served as props in his story. That's probably as far as creators ever allow it to go.

UPDATE: Steven adds a few examples, but I am not familiar with them.