Well, "ordinary" doesn't necessarily mean common. She's, uh... theoretically unspectacular in comparison to the other magicians around, who are youkai and have more inherent power. She's also ordinary in comparison to the other important human characters -- Reimu's the dang Hakurei shrine maiden, who the hell knows what's up with Sakuya, there's god-descendants and half-ghosts and immortals, and all of them have their own special super powers. Marisa, as far as anyone knows, is just some girl from the village who happens to have learned magic. So she's an ordinary person by nature, extraordinary only through her choices and actions.
At least that's how I've always taken the title. Either way, there's certainly a touch of irony to it, seeing as she is weird and unusual despite being ordinary, and those choices and actions have propelled her above some of the other people's extraordinary natures. Finding double meanings and sarcastic readings for character titles is entertaining anyway. (Perfect and Elegant Maid always comes to mind...)