If I wanted to be honest, I'm not especially enthused by the thought of Makoto as a character. Try as I might, I just can't get excited about however I expect him to play. Maybe I have a limited imagination, but it's just... sword guy? Sword guy with punching? I don't know, even if we're talking about bringing all of his other weapon options into it, I don't see a lot of appeal in a moveset based around dipping a bunch of fingers into a few other perfectly good pies. That said, I would be really interested to see him in the story regardless, assuming we take the Nyarlathotep angle. Would be a cool way of killing two birds with one stone in terms of fanservice, too.
FeMC would probably interest me more from a fighting angle, and I'm not being cheeky - it's just that the naginata is a much more interesting and distinct weapon to base a character around than most of Makoto's theoretical options.
And I definitely don't think it'd be impossible (or really, even particularly hard) to give Margaret her own, distinct playstyle from Elizabeth. There's a lot to the Velvet Room angle that Elizabeth in P4A does not necessarily explore. Margaret very easily could.
She's right, though.