I respected the way Janeway was conveyed as a Captain but also as a woman. I think Q made a cute comment or two about females running a ship which was actually amusing but mostly when Janeway conducted herself in the role of Captain that is what it was. She didn't have to, the script didn't have to, reference back to her gender. Pat itself on the back that she was breaking the glass ceiling. That is smug when that happens.
Yet equality should be about opportunity and deliverance and response. Not about pretending that the genders are the same. Treat them the same but they are different. Had the Voyager CO been male and written with the same dialogue it would have played differently. If Picard was female that would have played differently. Even when Genevieve Bujold played Janeway it translated differently. I really think that Janeway being female made her a better Captain for the journey Voyager made. How she related to others was enhanced by being female, just as Picard took command in the only way he could, being a male Captain. He suited his role too. Not so sure they would or should be interchangeable though. No doubt they would serve interchangeably but succeed the same.. no. It would be different.