It kind of happens to me a lot.
I have pretty much always been annoyed by Marius and Cozette since I read Les Miserables. They're okay, but Eponine is just so much cooler. She's clever, a little bit funny, and most especially, not wishy-washy and spineless like Marius and Cozette occasionally are.
Look at Lord of the Rings as another example. I would be more than okay submitting that Frodo is pretty much the least interesting character in the series. Aragorn is pretty epic, and Gimli is hilarious, but you know who the best character is? Samwise Gamgee of course! His loyalty, stubborness, optimism and just all-around Hobbitness make him the best of all the things.
Or take Harry Potter. Harry himself is pretty cool, but I personally find characters like Snape and Remus a lot more interesting.
I think I've discovered a similarity in all the stories in which I find secondary characters a lot more interesting than the MC's. All of them are Ensemble stories. They rely on a big cast. Harry Potter, LOTR and Les Miserables all have a host of intricately woven character arcs. In Ensemble stories like that, I think it works to have a more neutral main character, because they sort of act as the nucleus for all the crazies running about around them. Maybe Sam and Gandalf and Aragorn are cooler than Frodo, but their stories and their coolness sort of revolve around Frodo. Same with Harry Potter and Les Miserables.
My roommate and I went to the new Captain America movie last night (SO GOOD!) and without giving away any spoilers, probably my favorite moment was when a very minor and very terrified secondary character chose to stand up to the bad guys even though he literally had a gun to his head. So even though it was a very hero-centric movie, and I absolutely adore Cap, stories can still be enhanced by emotionally engaging secondary and minor characters.
And I can't help but leave you with my favorite song from Les Miserables, in large part due to the soul shakingly good voice of another E character--Enjoras.
What do you think? Are there secondary characters that you like better than their main character counterparts?