Romances
Usually I am very stubborn with relationships in things I enjoy. I think (like Shinjiro) that they tend to complicate things unnecessarily. Mitsuru, on the other hand, needs someone to rely on her and needs to rely on someone else. She needs people because she has spent much of her time isolated or alone. I've often talked about Mitsuru's relationships with my sister Cherri and every time I say the same thing. I can support Mitsuru with Akihiko, Shinjiro, or M Protagonist easily. I can see her being legitimately happy with any one of the three.
Aragaki Shinjiro
I believe that Shinjiro and Mitsuru would have been a great couple. They would have supported each other and been a great duo for caring for SEES. In general, I feel that they would have been good balance for each other because they have similar ideals and values (look after everyone, make sure they eat right). Shinjiro is someone that needs to protect others, Mitsuru is someone that needs the strength and pillar of support. Together, I think it would work out well. She would be forgiving of things that happened (which he needs). He would help Mitsuru branch out and try new things (which she desperately needs). She relies on him a great deal and feels relieved when he returns, so I can see how she might develop feelings for him. He would also be good for her in the terms of where she won't stand up for herself, he'd take care of that. Whose ass wouldn't he kick? At the very least, I can see that their relationship (romantic or otherwise) would be built on mutual trust and respect in which they both cared deeply for the well being of the other.
Sanada Akihiko
Akihiko and Mitsuru already have a very involved relationship. They know each other well and offer each other support and friendship. Mitsuru knows when he's over done it and forces him to behave. He knows when not to step on her toes. They have an understanding that cannot be ignored. Their knowledge of each other is deep. When Mitsuru needs help, Akihiko is there. He shares her joys, disappointments, and depression. And in all honesty, if not for being able to date Mitsuru with M protagonist, I would have assumed that Akihiko and Mitsuru were already dating - they're that close. I could also be led to believe that they are simply close friends because Akihiko wouldn't know the first thing about girls (as he has trouble dealing with them). In fact, I think that Mitsuru and Akihiko have a great dynamic, they work well together, they've been together for a long time. There is something there, whether it's romantic or otherwise doesn't matter. They are friends at the very least and they work very well together. How else would SEES have survived as long as it did? He makes decisions, Mitsuru doesn't overrule them. Their understanding of each other opens up a great venue for communication and mutual trust. I think his somewhat brash behavior would annoy her, but only because she genuinely cares about his well being. I think that Akihiko gives her a safe place to be and allows her to be more of her "true" self than when she's with others too. I also really like that her element is ice and it happens to be Akihiko's natural weakness (which he comments on). He admits himself that Mitsuru is pretty much his weakness and he wonders about that. Akihiko shows a great deal of concern about Mitsuru when the group is reunited after finding Fuuka. Mitsuru is being attacked, but he doesn't know where to intervene. In the game, she's thrown aside, but in the manga he catches her. I think that there is much that could said about their relationship. When Yukari confronts Mitsuru about lying to the group, Mitsuru states that "Not everyone has the choice" to which Akihiko promptly responds, "Mitsuru...Don't." He knows more about Mitsuru than anyone else and he knows that although she had her persona more or less forced on her, she blames herself for the things that have happened. He tries to protect her feelings and chooses not to engage Yukari. I think he wanted to protect Mitsuru but didn't know how to step in. Whatever secret that she has from the younger members of SEES, Akihiko knows about. He shows no surprise when Mitsuru mentions that she has been hiding information because she didn't find it relevant to their task. I think his concern for her well being prompted his silence. At the very least they care about each other's well being. If pursued, I think they would have a very deep and interesting relationship. They already have a great friendship - and would it be that bad to be with your best friend?
Male Protagonist
As the only actual romance partner for Mitsuru, I thought this would be good to include. I actually strived and studied to achieve this social link when I first played. Mitsuru values high academics and refuses to hang out with M protagonist until he has maxed academics and makes it to the top of his class. She values that he can attend to all of his duties with none of them suffering. Through the Empress Social Link Mitsuru becomes very close to m protagonist. She falls in love with him because he helps her to see that she can make good choices for herself that are not detrimental to Kirijo Group. He puts Mitsuru first and it helps to boost her own confidence. She comes to rely on him a great deal. Her reliance on him, however, comes long before she is romantically invovled with him. She trusts him as field leader of SEES and is astoudned by his use of multiple persona. Through him, she is finally able to achieve her goal of stopping dark hour and uncovering the truth of Tartarus. But there's more to their relationship than being used to achieve her goals. She stands up for him when her (arranged) fiance bad mouths him. And she decides she should make her own decisions after spending time with him (something I think she admired about the way he did things). I think that he saw Mitsuru needed a push, he had a very different understanding of her only getting to see the leader of SEES. He showed her how she could be a leader and make decisions that still benefit the self without either suffering. I think he served as a great example and that they would have been great as a couple. He would have been there to remind her that she can do anything and that he'd always be there to support her. He also has the benefit of being younger than her (which might translate to needing to be taken care of) which Mitsuru would welcome openly. She could dote over him much easier than Akihiko or Shinjiro who are equally stubborn.
Other
I've also seen some people support her with Yukari. But, I'll be honest. I think that Yukari was the first female friend that Mitsuru had. Yes, they cried together. But they had an understanding for having lost their fathers! Was there romance? I doubt it. I think that people can have a deep respect and love for each other without being romatically involved. Mitsuru does envy Yukari's freedom in fashion, but I think that stems more from the fact that Mitsuru has people that pick out her clothes. Mitsuru's choices for her self are much rarer than the choices she gets to make for family, duty, or SEES. I believe what she truly desires is freedom to be herself. She gets that through her friendships and I think she already has that with specific individuals.