See my reply to Kaldric - the Bechdel test is very limited on individual movies, as you can prove with hundreds of examples of both movies that failed it while having genuinely strong/deep female characters, and movies that passed it while having nothing of the kind, but I don't think it's really intended for that.

If I understand you right you're saying that the all-boys school was much better academically also? That's odd because statistically, the general conclusion is that while girls perform significantly worse in coed schools, boys perform significantly better. At least that's what I've always read. Having been in an all-boy class inside a coed school for two years (our system is a bit different, students generally have all classes together with the same people), I can definitely confirm that the difference in atmosphere was noticeable, although I'm not sure the effect on academic performance was that big - it certainly wasn't a positive effect, though.

I have to strongly disagree with "your male audience simply does not feel welcome" if two women talk about something other than male characters. For starters, I would assume that you didn't actually mean to go that far, and that the "not welcome" part applies only when the women are discussing topics that are seen as specifically female topics. Not in cases like the Guardians scene which you mentioned, with the women discussing the mission in exactly the same way men would do. But even with that assumption, I still disagree, and in fact find it a little offensive. Yes, men and women are different, but then isn't the whole point of a movie, or a book, or any kind of fiction (or history/biographies) that you learn about the things happening to people other than yourself, and learn how these people different from yourself look at things and handle things? If a man walks through the ladies room, the main reason he feels unwelcome is that he almost certainly is unwelcome. Watching women on screen having precisely the same conversation - why should he feel unwelcome or turned off? He might on the contrary find it very interesting and gain a better understanding of women, just as if he read about it in a book, fiction or otherwise (though presumably the book would teach him more).

And I don't think I agree with your commercial conclusion here either, that the off-putting effect on the young men, just because there's something in the movie that they can't really relate to, would be bigger than the positive effect on women who feel that this at least is an action movie that takes them a bit more seriously (talking generally, not specifically about Alien II as I haven't seen it). It seems unlikely that there would be much of an effect on box office in either group, it's more a matter of how enthusiastic the people would be afterwards. And I do think there the positive effects would outweigh the negative.

To take a completely different example from a completely different context, the Lord of the Rings movies had a good amount of little details that were essentially meaningless to people not familiar with the books - but it's not as if that group of viewers felt particularly alienated, while on the other hand, the big fans of the books appreciated those enormously. I would say in general, it's often a good idea to make that kind of concessions, even if it makes the majority of your audience feel like they're missing something - that on its own is unlikely to turn them off your movie, while for the minority it may mean a lot.