Mine's Diddy Kong while my secondary character is Shulk but I rarely use him anymore. And here I thought I was going to main Villager and possibly Mega Man.
I don't have a main really. I mean I only really play Classic and Smash Run and I use whoever I feel like. Though I would say that my main is Ness. I wanted it to be Mega Man, but after a while he felt a little awkward. I feel like once SSB4 comes out on Wii U, I'll have a better answer though. I feel like it'll be Ness anyway, but we'll see. I feel like I need the Wiimote/Nunchuck combo since I'm used to that. I kind of have a hard time with the 3DS controls.
My main is the same as it's been since I first picked up Smash Bros back when Melee was new: Yoshi. Aside from a few slight changes that took some getting used to he's better than ever and I love that. Online I also use Lucina, Robin, and Greninja frequently, so you could call them my secondary mains.
I sort of liked Olimar but with the newcomers I like Little Mac, Rosalina and Luma, Meta Knight most of the time (online), but sometimes I like to mix it up with all the characters. I usually like characters with a lot of useful options like counter or super armor.
My secondary main was my main for all three installments: Samus. My main, however, is now the Mii Fighter. Specifically, the Swordsman. I also use Pit and sometimes Link/Meta Knight.