Seems to me Mary's hinting at marriage. Remember, fairy tales end in "happily ever after," (or at least the ones girls like do,) and that was her reference.
I agree here.
From the beginning talking about "winter days that will fly by..." to a chilly near-autumn night... Well, that would mean a span of... like 9, maybe 10 months... 2 exam periods, too. Yeah, they came together later, but still, they spent a long period of time together.
In the monogamous route, starting with the decision the MC did NOT cheat, letting the threesome not happen and ignoring everyone else, Mary's question about how it will end is clearly about things like moving in together(well, yeah, they kind of did, but officially... I don't really know...). Mary mentioned this earlier during their trip. "Ours" is the word that comes to my mind here. And yeah, marriage, starting a family... These are the things Mary wants to hear about, and is not having thoughts about breaking up or something.
Here is why: Let's put aside that it's a seaxual game and look at it a bit realistic: Mary is in her first sexual relationship, tries out things she never did before, because of MC's influence I guess... Even anal. Beside of porn, anal is still something very intimate, something you just don't do with anybody, not even with your partner maybe... Analsex and thinking about breaking up... I don't think so... Their relationship stood strong against Andi's antipahty and the appearing of the ex who either cheated or was cheated on. "Us against the world" did Mary mention, if I remember right...
I think going the threesome route is creating these negatively charged opinions about possible negative outcomes... Yeah, this route offers the "most" sexual content to have, but this might not be the "right" way... The decisions leading to that are causing cracks in the relationship I guess. I played it, too, wasn't mine, tastes are different... But I think this route might end in a bad ending (or a good one, depends on you
)
But what the devs are planing is a whole other thing... Maybe there will be different endings depending on answeres and routes chosen, some of them could be bad ones... If you want MC and Mary stay together... Well, I think your route should only include her and nothing/nobody else... If you want anything else, feel free
But I think we all agree that it's a great game!