Micaiah gets called the Mary Sue because of her special abilities, status, the whole incident in Part 4 and is forgiven quickly for her previous actions, so people throw the Mary Sue term at her. Ironically, they ignore that the game beforehand criticized those actions, highlighted her mistakes and even her allies were quick to call her out so she wasn't treated as a perfect or idealized character. Hell, if it wasn't for Part 4 (or at least, if it was written better), she probably wouldn't be called a Mary Sue at all.
Ike does fall into the category of an "Idealized Character" a bit in RD as he has no flaws, no drawbacks, the game heaps praise on him, he steals the spotlight from Micaiah and so on, but again that does ignore all of the things he did to get there in the previous game as he grows there and starts to become a better leader so there wasn't much more for him to grow. They could've been better about balancing his story with Micaiah's, but he's still not really a Gary Stu when you take in everything the character has done.