(Cross-posted from my dA, like all my stories are cross-posted from FFnet.)
Well, maybe not immediately, but definitely after whatever BBC does for EMPT.
"What's this?" certain readers cry. "The Slash-hound supports a Het pairing?"
Actually, there's several I support, but I can see where this would come as a shock, considering that there's maybe three het-ships among my long, long shipping list.
Lately, however, I've been considering, and even with all the fun ship-teasing that goes on in the show... Sherlock, at least the BBC version, is really written to be asexual. And I honestly believe John when he insists he's straight -- maybe more of a Kinsey 1 than a 0, and he might be open to some experimentation down the line, but, physically, attracted largely to women. And you know what? Both of those are completely okay, and oddly enough, still fit completely into my fanon. Because Shwatsonlock, no matter the incarnation, is about far more than mere sexuality -- it's about the commitment and the intimacy, about the Companionate Love that I would challenge any fan to deny that they have for each other. (Except in adaptations that completely miss the point, like the Roxburg HOUN.) So, there's that.
Then there's Molly. I've been a Molly fangirl since shortly after seeing Great Game, after a random picture on dA made me consider her character a little deeper and realize that she isn't just a reflection of the horde of fawning Sherlockian fangirls -- she had the potential to be really amazing, if only she was given the chance. Thereafter, Molly getting her 'Let's Get Dangerous' moment became something of a theme in several of my (yet-unfinished) stories. (Validation for this Molly-fangirling has come with 2x03, The Reichenbach Fall. Hell to the yes. <3 )
Anyway, get to the point, right? What does all that have to do with Molly and John getting married?
Well, as a few people might be aware, my main ship in Holmes fandom (focusing on Canon and Granada) is Shwatstrade -- Holmes/Watson/Lestrade. Oddly enough, it's the concept of a similar dynamic that leads me to ship John/Molly.
Simply put: Both of them would understand that Sherlock comes first. John and Molly both are heavily emotionally invested in a man who is virtually guaranteed to never feel romantically inclined towards either of them -- and this is a problem, because this emotional investment colours and disrupts all their other relationships. Neither of them can manage to carry on a relationship with anyone else because they're too ready to drop everything and run to Sherlock's side the moment he needs them. Sure, they'll put up some arguments, but in the end, Sherlock trumps.
Additionally, although Sherlock may be asexual (or at least, in other adaptations -- and in my Shwatstrade stuff -- possessing of a very unobtrusive libido), it's obvious that he feels very protective of those few he becomes close to, and even (subtly in canon and less subtly in certain adaptations) feels very jealous and possessive of them. This was a point of serious contention when it came to Watson/Mary, and when it comes to Watstrade and Shwatstrade interpretations. However, since he, in all likelihood, files both John and Molly loosely under 'Mine', and since he clearly trusts them both, he's unlikely to feel threatened by their marriage, as he might if either (particularly John) somehow managed a serious relationship with anyone else.
So, yes, it would not be marriage of romance or passion; it would be a marriage of practicality, comfort, and companionship. Considering how many 'romantic' marriages end in divorce, I don't feel particularly bad about suggesting one that isn't very romantic.
As to compatibility, since that's kind of important in a marriage, John and Molly are both very nice, very sweet, very intelligent people with mediator streaks, who already have a history of friendship; both are medical professionals but in different fields, so they have further common ground but probably wouldn't have rivalry issues; neither, as far as I am aware, have any odious personal habits that couldn't be worked around. Molly has Toby, but John hasn't displayed any distaste for cats in general (the Sphinx doesn't count, even some cat people think they're creepy). Sexual compatibility may or may not be an issue -- Ultimately, I don't think they'd be particularly passionate, but without that pressure, I can see them becoming very comfortable and even playful in bed. The best thing would probably be to keep it an open marriage, of course, so that sexual compatibility can be found elsewhere, but both of them strike me as very monogamous, so I consider this unlikely. (Well, monogamous until such time as Sherlock expresses interest one way or another, at which point all bets would be completely off.)
Jealousy over Sherlock's attentions would, of course, be the major source of contention for this pairing. Optimistically speaking, I think both John and Molly would be able to work around that (perhaps even with Sherlock's help, if he manages to clue in to their emotional well-being), but it would probably be the basis for most of their fights.
I'm undecided on whether they would be more likely to try and get their own place, to just move Molly into John's room in Baker Street, or to get a larger place for both of them and Sherlock. I'm leaning towards Baker Street, even if it would be a tight fit, but that's just because the possibility of them leaving behind either Sherlock or Mrs. Hudson just seems wrong.
Edit: After some consideration, Molly and John should fix up and move into 221C. That gets rid of the issues of leaving behind either Sherlock or Mrs. Hudson, but allows them the space to set up a home and family (and to keep Toby) without all of Sherlock's experiments and weirdness being directly in the way. (Also Toby + Sherlock's experiments just seems like a bad combination.)
Edit2: So apparently 'Molly' is actually a pet-name version of Mary. BRB squeeing forever.