I agree with pretty much everything you said - for a real world setting. Since the MC is the "MC" of the story, he's going to get opportunity/position/respect etc. that he hasn't really earned or is ready for. As the "Main Character" of a harem game it's pretty much given that he was going to be the leader from day one when he was a TOTAL loser. Would that happen in real life? Oh Hells no! If you think about it, Harry Potter is just about the worst "leader" or "hero" of almost any piece of literature.....ever, yet he
was the leader and hero because he was the MC of the story. All of the girls in this story are smart and capable.....until they're suddenly not and need the MC to make things right ( I know that has to drive you up a tree
).
As to Riley (my favorite actually) she
was the best choice to be the leader - in the past. She handled herself very irresponsibly during her return to "active" duty, which is why Queen Unbreakable had the MC fight with her so show her that as capable as she was - her mind wasn't in the right place.
The only thing the MC has over the others as far as leadership is that each of them tends to be a loner and not work as a team with each other. Since he has some level of relationship with each of them - he is a common thread to bring them together. To go back to my "Harry Potter" scenario - everyone else in the book was smarter, stronger, faster, more powerful, and less of a bumbling idiot that he was - but
he was the binding that brought them all together. Everyone here, including the cat, is better at pretty much everything than him - but he is the glue. Hey! that can be his superhero identity -
GlueBoy!
I initially stated (mostly as a joke) that this was just a test by QU to make him "man up" and take the lead and force his powers to manifest. Since one of the girls, don't remember who, said almost the same thing about it being a test by QU, I think I was wrong and this will be an actual "bad guy" situation.
Just my take on it.