Holmes himself has Gary Stu-ish aspects, but I don’t think it’s the male vs female debate that’s relevant there, it’s the fanfiction vs canon problem. There are canon protagonists out there which have suspicious traits in line with being fantasy versions of the author, but they’re more likely to get away with it. Possibly because published works tend to be of a good story-telling quality that compensates for the Sueishness, whereas most Sue/Stu fanfics tend to be a poorly disguised personal fantasy being shared.

In a way I think my issue with it is the very opposite to yours, actually: the problem I have with it is that I think as characters they had a lot more potential for sexual tension…just not quite as things were played out in the books, because it would have made the father figure sense of the first book way creepier. If they’d been closer in age that might’ve nullified the father figure thing, or if they’d met when Mary was older, but either way I think ignoring any sexual relationship between them at all actually doesn’t do justice to how interesting a pairing it could be. Even if the point is that they don’t have a sexual relationship – you still need to mention it at all to get that across.

In general I think if Mary had actually shown more of a sexual side that it might have rounded her character out a lot more. She comes across as a bit hypocritical sometimes when it comes to feminism and emotion – which can be an awesome point that King explores, or it can leave her a bit wanting as a character, and I think it tends to the latter more often than the former.