Jesus fucking Christ. Reimu isn't a mary sue at all. And I think the reason why you think she is, is because your only looking at one part of her character.
Read WaHH, where she is NOT sueish in any way, shape, or form. In that manga, she constantly makes mistakes, fails, makes a fool of herself, and is generally just an all around dumbass.
The only sueish thing about her, as you mentioned, is her power. And a powerful character isn't automatically a sue BTW. Because even If she can't lose a fight, she isn't so successful with other things.
(This was written late at night btw. So sorry if this makes no sense.)