I usually play female characters because meh, I prefer to. The "why" of it probably has a lot of factors. I find it very interesting to see what the developers have put into making you a female, if anything, or if it's merely a model/voice change with nothing added or subtracted.
You almost, but not quite, have a good point going. The spectrum of female strength and speed does not go as high as a male. The average male will in most cases, with similar amounts of training and exercise, be stronger and faster. The difference is noticeable in high-performance sports; there's a reason women compete against women and men compete against men in the 100m sprint, for instance. So yes, at peak unaltered condition, you have a fair point.
But being a hero, protagonist, or even PERSON, is more than your maximum weightlifting potential, and how many people are at peak physical condition? And WHEN? You can't be at peak condition all the time. Athletes know this, that's why they try to top up their form just before important events. Most people aren't NEAR peak condition at any point in their lives. I'm six foot four inches, overweight but quite strong. I don't know ANY women who are as big as me (luckily for them), and none as strong either. I know several who can kick my ass. If I trained as much at martial arts as them, or even a little less, and got in better shape I might turn that around, in fact it's likely, but I don't.
Then there's force multipliers. Put a gun in a woman's hand, and she's effectively just as deadly as a man. The only applicable factors now are that she's strong enough to hold the gun, which is NOT too high a bar. Then her ability to aim, her eyesight and her reaction time; women do just fine with that, and her bullets will kill you JUST as dead as a man's.
Women not being able to be as threatening as a man is lazy writing and stereotypes, and that's all. That a threat of violence from a woman is less threatening to you than one from a man is because YOU find it less likely that she can and will carry out the threat, based on your experiences. Those are societal behavioural norms. Let's say I'm a criminal trying to run from the police. A police officer tells me to freeze, and levels a gun at me. How do I decide? Well. Are there innocents in the way? If so, the officer is less likely to take the shot. Is there cover nearby that I can use? At no point does it concern me if the officer is male or female.
Now, in Mass Effect I agree on female Shepard being... less enjoyable. Even I, who usually play female characters, couldn't in that game. That was mostly because I found the female supporting cast and potential love interests hugely more interesting than the male ones. I don't get why you'd have a problem with a sci-fi supersoldier being female rather than male, really. Your example illustrates my point perfectly. Female Shepard knocks a Krogan down with gun butt, you disbelieve. Sure, I'll accept that. Male Shepard knocks a Krogan down with gun butt, I disbelieve. Krogans are unstoppable monstrosities, more hardass than any other common species, and a HUMAN knocks one out? You'd have trouble slowing one DOWN with less than two mags! Now, in a world with cybernetic implants, powered exo-suits, collapsible high-powered weaponry, and goddamn magic (Mass Effect Fields are essentially that), you're concerned because the raw, unaltered character might bench press slightly less than if she had been male? No. I don't get it.
As for flames, yes you are and will be getting them, which I don't see any reason for. While clumsily put, your question is valid, and merits discussion, if nothing else then so we can reach a greater understanding and come together as one brotherhood of man and... then there'll be cake. Probably.