I don't see Mitsuru as a Mary Sue at all. I mean, yes, academically and "professionally" she's damn near perfect, but in terms of interpersonal relationships, she's not that great. She's bossy, domineering, and brusque in her social graces to a fault. Decisiveness and confidence are great, but I would have a hard time following a leader as bossy, domineering, and somewhat lacking in tact as she is. Again, being hard-nosed isn't necessarily bad, but there is that old saying of attracting more flies with honey than vinegar, and she was all vinegar to me. Personally, I didn't like Mitsuru very much, but that's just me. I'm probably in the minority. I'm not the biggest tsundere fan, and Mitsuru is a tsundere to me. My personal favorite of the P3 females was Yuko Nishiwaki- the strength s-link.
Then again, games like P3 and P4 almost force you to make your main a "Marty Sue." One time I tried making my P3 character an idiot slacker, but doing so locked me out of at least 75% of the content, so I had to make him an academian again. You have to be an athlete, a scholar, a ladies man, everything or you basically get nothing out of the games.
And even coming back to taste, like I said in my Memories Off review, I didn't really like Shion Futami, yet she's the most popular fan favorite among the Memories Off faithful. Go figure, huh?