Twin Knights
Although Mitsuru can defend herself, I thought it fitting to include the first two friends I believe she had. She's not as close to Shinjiro as she is Akihiko, but both trust and respect her. I felt it important to include them as twins because of their persona Polydeuces and Castor (which could probably be elaborated by others, so just know that's why they're both here). In fact, I think that they are Mitsuru's first friends which is why she can be so sharp when speaking to Akihiko but extremely relieved upon Shinjiro's return.
Sanada Akihiko
Akihiko and Mitsuru have an extremely close and pointed relationship. They know each other well and they are there to support and defend each other. In Mitsuru's case, she's there to ground him and make sure that he stays out of trouble. Mitsuru is noticably snide with Akihiko after bringing the first large shadow to the dorms. He suffers from injuries which she has no problem calling him on. In fact, she has no problem telling him to rest or that he would be nothing but a "hindrance" for the Priestess Arcana full moon boss. In light conversation with the protagonist, he mentions that he wants to go back to club but knows that even though he wanted to there was no way that Mitsuru would let him. On several other occassions he states he's ready to go back (even though doctor hasn't said so) and Mitsuru promptly responds, "Are you trying to make me mad?" This ends all conversation and Akihiko let's it go.
His obedience to Mitsuru is grounded in respect and trust, I believe, more than fear of anything else. He knows that she's looking out for him and he tries to respect that. He always stops arguing with her when he knows she's brought up a valid point. He knows better than to be careless but doesn't often think of that himself. He's more concerned with not feeling helpless, so Mitsuru gives him good balance because she makes sure to pay attention to injury. I think they're close enough to say things like "You're being stupid, knock it off." But Mitsuru has a definitive way of speaking and instead implies it with her tone.
Their relationship is not all pointed, stop being stupid Akihiko banter. In fact, in the early months of the game you can see how close they are. Mitsuru stays up late on the second full moon to scan for shadows. Akihiko is surprised that she's still working on it. She admits that if she were better at it she wouldn't be a burden to everyone else. She seems disappointed that her ability has a limit, this is something she doesn't let anyone else see. Akihiko doesn't comment specifically on it because she finds a large shadow (I'd like to believe he'd support her, but I can see him saying something stupid too), instead he awakens the team. He constantly makes the decision to place protagonist in the leadership role (which he couldn't do if Mitsuru didn't trust him). I feel that he and Mitsuru have a very close and trusting relationship but he tends to be reckless. Also, with really important decisions he mentions on more than one occassion that he "already talked it over with Mitsuru". I think this shows that they communicate often and are actually probably much closer than we get to see. In fact, when Fuuka joins, it's ultimately because Akihiko insisted that she replace Mitsuru as support. He knows that Mitsuru is at her limit as well as the fact that Mitsuru's persona is more battle oriented.
That aside, her trust for him is obvious because she lets him see her disappointed and angry. She lets him see a great many more emotions than others. She's less guarded around him. I also believe that he relies on her a great deal as he in noticably shaken when her father passes and he has no idea on how to cheer her up. He seems almost as depressed as she is, because she is depressed. I think this shows a great depth to their friendship. As for how well he knows her, well, he states in the hot springs that if Mitsuru's there there's no way she'll consider it a misunderstanding (even though it is)! It shows that he knows how stubborn and resistant she is, he knows that she won't budge and that it'll do them no good to try and explain their case. He knows Mitsuru. Maybe better yet, he knows better than to fight with her. I also think that they are very close because Mitsuru worries about him. When he's late she believes she at least deserves the courtesy of a phone call.
Aragaki Shinjiro
If the protagonost is female, Shinjiro gets annoyed when asked to join the final time. He states "First Mitsuru, now her." He tries to explain to Akihiko that they have to protect girls, but the boxer doesn't seem to understand that. For me this shows he feels a sort of obligation to look after women, I think, because of Sanada Miki from his childhood. He doesn't find women in general annoying, he does find girls to be nothin' but trouble though as he mentions to Junpei at one point. Despite finding females to be troublesome he does try to protect them. This is shown when Yukari convinces the others to go to the alley to find information and Shinjiro steps in to assist them (I rather think that he stepped in to save Yukari and F Protagonist than to save M protagonist and Junpei). He even goes so far as to scold F protagonist, but I don't believe because he's angry (definitely annoyed). I think part of him just needs someone to protect and he does so. I also believe that after the death of Ken's mother this desire grew bigger but he wasn't confident enough to actually do it. This is why when Mitsuru says she is relieved that he is back, he tries to brush her off. But, he does do everything he can once he is part of the team again. In the manga, he asks if his room is still there, Mitsuru mentions no one has been in there and nothing has been touched. But he seems certain it must've at least been cleaned. In the game, Mitsuru can be seen standing next to Akihiko upon Shinjiro's return. She wears a soft expression and mentions her curiosity of his return. She also mentions that she won't pry, which Shinjiro appreciates and says he might tell her one day "if he feels like it." They have a good understanding of each other, I think. At the very least, they know when to leave things well enough alone.
I believe that if truly elaborated on, he and Mitsuru would have a fairly good friendship. He has huge expectations of himself and others just as she does. I've also always wondered how he dresses so nicely despite living on his own in the alley (it's always been my secret belief that Mitsuru still looks after him and he has to accept the help because he knows better than to make her mad). Unfortunately we don't get to see how close he and Mitsuru are, but the fact that Mitsuru states she's glad he's back makes me think that she relied on him a great deal. He was one of the first comrades she had. I also feel that she probably offered support the night that Ken's mother was killed and because she was unable to scan and support as much as she'd have liked, she blames herself for his leaving. She might even feel somewhat responsible for the wedge between him and Akihiko but has no idea how to intervene and help. The interactions we see with Shinjiro are based with Akihiko.
Based on the f protagonist route we get to see a much softer Shinjiro. I think if given the time to accept, heal, and be forgiven he would have been a very good balance and protective figure to SEES alongside of Mitsuru. It's a shame that their friendship didn't get more elaboration. I think that he and Mitsuru would have had a lot to talk about in terms of caring for SEES and the best ways to do it.