Aerith wasn't a Mary Sue in the original game, and there were definately faults present. For AC/ACC, part of it was lack of screentime and another was that she was dead, and apparently at peace with herself (though she did worry about Cloud and such). In CC, we really don't see that much of her. When we do, it's bonding experience between Zack and her, and then at the end to really make Zack's death pack an even larger punch. She really doesn't have much of a reason to show these faults, though I guess clinging to a man for many years, with him not contacting her at all, can count as one...depending on how you look at it. It could be seen as an inability to move on (which is later shown in FFVII), though it's a bit hard to step back and see it like that when we know Zack existed and what happened to him. It's more of POV weakness/fault. I don't know much about her in BC, either, but she appeared in what, one episode?
Overall, I just think it's her other appearances that give her a more Maru Sue feel. In those appearances she was either A) dead, B) didn't appear much, or C) didn't play the type of role that called for those faults to serve a purpose.