So I made an off-hand thought about Touhou's 'main character'.

[Suspicious person]

Guys
You sure Reimu isn't the main chara just because

Spoiler:

ZUN said so

or something

[Tengukami]

people think sanae is reimu's luigi because she's green and is a shrine maiden

This is my understanding, too. My non-joking take on this comes from looking at the dynamic that Reimu and Marisa have. Without going into great detail over this, Reimu and Marisa have this "double act" thing going on; i.e., Reimu is the "straight man" and Marisa is the "banana man". Where one is somewhat stolid and duty-bound, the other is freewheeling and comically selfish. Their dynamic seems to be loosely based on this classic "trope", if you will, that is sometimes used in pairing up two protagonists. Marisa is Laurel to Reimu's Hardy; the Costello to Reimu's Abbott. It's a fairly widespread dynamic and, in my amateur opinion anyway, explains in part why Reimu And Marisa maybe "feels" like a natural thing to a lot of fans, that their dynamic touches upon this in its own way.

[Clarste]

I think the fun part is that it's actually more complicated than that, since Reimu isn't always the straight man, nor is Marisa always the comical one. While sometimes it's the way you describe, in other cases Marisa's the one with common sense while Reimu's casually breaking social conventions because she just doesn't care. They have an interesting dynamic where they're pretty much always going to respond to things in different ways.

[Tengukami]

Totally! That's what I think makes it so much fun; the added comedy of when they switch their usual roles.

[Starxsword]

Reimu is player 1 and Marisa is player 2. As the others have said, kind of like Mario to Luigi.

[Tsuken Yasashi]

I think of Marisa as the "Player's relationship" to the story, where we want to be part of what's happening in each game.  Considering the fact that she there to 'steal' Reimu's job (or just to have fun while the incident is happening), it kind of plays off of us that we, the player, would want to share the burden with the shrine maiden to help her in her adventure, or just at least be part of it and possibly do more than the shrine maiden.  Though carrying a job alone is possible to the human mind, the amount of responsibility can be overbearing to handle it alone, hence Marisa is there to help her friend out.