Mary is an assassin. Mary is an assassin who, on at least one occasion, seems almost amused at the moment she was about to kill a more or less innocent man (Sherlock). She is cold and a bit cruel, certainly not gentle or easy to like. And after seeing what Sherlock’s “death” post-Reichenbach did to John, she still shot that same man in the chest rather than let her secret get out, then threatened to do it again at Leinster Garden. That’s a hell of a lot of moral baggage to make sense of. She’s dangerous and not good for John; that’s actually the thought that brings him back from death’s door. But at the same time… she seems to let Magnussen call for help as she’s talking to Sherlock (and yes, she would have seen this; remember the mirror behind Sherlock). Sherlock took time while he was bleeding out internally to try to reconcile her and John. He was willing to risk jail to give John the life with her John wants, and when he knows he’s being sent on a suicide mission he doesn’t make a last-ditch effort to warn John off Mary. He nearly confesses his love for John and then makes a bad joke about baby names - just after Mary says she’ll look after him. If Sherlock still thought Mary was a danger to John, this seems like a massive failure as a friend.
All of which makes me think that Mary is complicated. She may turn out to be a complete villain. She may turn out to be the true Moriarty who’s been pulling the strings on Richard Brook, for all I know; or she may be an ex-assassin who was doing one last job so she could safely retire to be the charming doctor’s wife in the suburbs. Frankly, both possibilities seem boring to me. When I dream about my ideal Mary, the version I’d like to see become canon, it’s someone who was and is an assassin but chose people she agreed deserved to die - an assassin with a moral compass who has some connection to Mycroft and was probably involved in St. Bart’s in some capacity in return for immunity for past crimes. She’s not nice and I don’t want her to become soft, but she’s also not so irredeemably evil that we get to put her comfortably in the villain category.
I want this version of Mary Morstan partly because the only way I can be comfortable with the ending of HLV, at least the only way I’ve dreamed up in the four months since I first saw it, is if Sherlock learns something about Mary between his getting shot and that moment on the Tarmac that makes Mary seem like a good protector of John. None of the other options are pretty: either he knows she’s bad and is so messed up (depressed, suicidal, whatever) that he leaves John Watson to her - or else he knew about the whole “Did you miss me?” stunt and the whole Tarmac scene becomes yet another emotional manipulation of John Watson like St. Bart’s and the we’re-about-to-die moment on the subway car in TEH. If that’s the route we’re going with Johnlock, Sherlock using falsely high stakes to push John into a certain emotional reaction, that’s another red flag I’ve seen in the DV shelter. On top of which it’s just repetitive storytelling. To borrow Sherlock’s phrasing, having John think Sherlock’s going off into certain danger when Sherlock and Mycroft have already worked it all out? That’s so two years ago.
I could be wrong about my personal hopes for the direction Mary Morstan’s character is driving in. We all could, with this show in particular - Team Moffat seems to take great pride in misdirecting us, and there’s just so little we know for sure about Mary’s character. But my point here isn’t to argue that my personal hopes and expectations for Mary’s characters are correct. It’s to put myself out there is at least one example of someone who thinks Mary’s a difficult character, who understands why people would be completely turned off and want to paint her as a villain - but also sees good reason to think (at least hope) Team Moffat won’t go full-out evil villain with her.
Put more simply: there’s a third way. Mary can be flawed, difficult, and not a suitable love interest for John Watson - without that meaning she has to be evil.
If you want more context on what prompted this discussion, you can read a bit more at my original Tumblr post; but I hope it's not necessary.