Savior
The protagonist can be male of female and serves two very distinct roles based on gender. If the player chooses to play as a male, he is the leader and can be Mitsuru's boyfriend. If the player chooses female, then she is the leader and Mitsuru's "sister". Either way, the protagonist serves as a grounding force for Mitsuru. Protagonist has an interesting ability that allows them to summon multiple persona. This is most likely what keeps them as field leader of SEES.
Protagonist leads initally because Mitsuru works support and Akihiko is injured. Protagonist is the first one of the new members that summons persona. The will to fight and pull the trigger on the evoker seems to place them in a good position. After Mitsuru and Akihiko both join again, there is little reason to change field leaders. This shows, I think, how much Mitsuru trusts protagonist's judgment. She knows that protagonist can do what needs to be done. I'm certain she feels relieved by their ability to make quick decisions. Mitsuru often feels useless and when the protagonist is still able to assist, she feels more confident about stopping shadows and the dark hour.
The social links for male and female protagonist are almost identical. The main difference is that rather than confessing her love to female protagonist she states that she feels as though she has gained a sister. The point, however, is that through the protagonist's support Mitsuru becomes more confident, ditches her jerk of a fiance, and starts to make decisions about her life and Kirijo a lot more. Mitsuru gains the confidence to make her own decisions, she becomes less critical of herself and tries to step out more often. She doesn't need to worry about what others think, because she is a smart and determined woman. The friendship with the protagonist helps her to step up to the challenges of her life as the new head of Kirijo.
I feel that Mitsuru's trust in the protagonist is what really helps to make her open up. Without them, I feel like she wouldn't be able to move forward. Not just because of their relationships with her. I think that the protagonist's influence on the rest of SEES also makes them more understanding of Mitsuru. In particular, when Yukari find out her dead helped to create shadows, Mitsuru wants to go after Yukari but feels she can't. She sends protagonist instead. This shows me how much Mitsuru knows about what she can do herself and what she needs other people to do. This is a very different step for the girl who takes on everything herself. In addition, I feel like Mitsuru knows who she can trust to do specific things. I think that without protagonist, she would never had trusted anyone but Akihiko and that they would still be fighting shadows.
Finally, I believe that the protagonist's sacrifice at the end and in The Answer, makes Mitsuru's friendships more precious to her. She understands how important loss is, and I feel that once you know it, you never forget it. With Mitsuru, I think it helps to push forward and that the idea remains close to her heart. That she can do things and there was always someone there who believed in her enough to give everything for her.