It seems like a strange question, but think about it. Is your main your favorite character?
For me, the answer would be a No. This isn't to say I dislike my main, I simply enjoy my alt more. My gut told me originally that I only thought that way because my alt was something I didn't get to play as much, something new and exciting. As the months went on, though, I came to realize that I simply like my alt better.
My main is a DPS class, my alt is a tanking hybrid. As most of my friends could tell you, tanking is in my blood. In WoW and other games, tanking is kind of my 'thing.' Its been suggested to me a number of times that I just change mains, making my paladin my primary character. I like the idea and considered it, but there are other things that have kept me from doing it. My guild needs a shadow priest for the raid far more than another paladin, and at this point in the game, there's no closing the gear gap to catch up and continue raiding with a new main.
There are other reasons, too. Emotional attachment is a big one. Its a bit shameful to admit you care for a character that much, but after three years of Warcraft, the thought of shunting my main to the background is a bit painful. Maybe that's just the roleplayer in me, but you never know! I'm sure there are PvPers that feel the same somewhere out there, right?
Am I the only one in this boat, or are any of you guys in the same position? Is your favorite character secondary to your main for one reason or another?