Bear with me, because my loath for Micaiah is a flash-freeze from 10 years ago.
To understand where this Mary Sue talk is coming from, first you need to understand that Radiant Dawn jettisoned a hell of a lot of plot points and character development from Path of Rafiance. Radiant Dawn is a story of wasted opportunities, and it all boils down to Micaiah and the Dawn Brigade.
Micaiah and The Dawn Brigade shouldn't exist. You could've removed either of them, and wouldn't have made a difference. Micaiah herself robbed certain Path of Radiance characters from stories that were rightfully theirs. These characters are.
-Mist, because of her ability to touch Lehran's medallion (Yune's vessel) without going insane.
-Soren, who is the rightful f*cking heir of Daein.
And yet, Radiant Dawn tosses Mist aside, and relegates Soren's bloodline to a super-secret series of support conversations that no average player will ever see.
Guess Micaiah's 3 major contributions by the end of the game?
-She is Yune's voice-box.
-She is the Queen of Daein.
-She liberated Daein.
Do you see where that whole "warps the story to fit her needs" come from? She was a literal fucking nobody, that got Ike's respect, Mist's Medallion Powers, and Soren's heritage all for herself by the end of Radiant Dawn. You could even say that Daein's liberation wad Pelleas' storyline. Think about it.
A whimpering King trust into leading the Liberation of a country that doesn't even belong to him by blood. Come chapter 3, and the Rightful King arrives, even if the later doesn't realize.
Pelleas vs Soren.
And once again, Pelleas is relegated to a plotline death (barring super-secret second playthrough) just so Micaiah gets her chance to be Queen of Daein.
And that's just the Mary Sue stuff. In general, Micaiah is just plain unlikeable.
In game-play terms, she's not very good and yet she's mandatory, not to mention she's surrounded herself with scrubs with low-base stats and outright game design mistakes. Look at Fiona or Meg. Look at Blonde Archer, or a late-game Sothe, who's also mandatory for those final chapters despite a Volke whose base Strength is greater that Sothe's Max Strength.
And story-wise, Micaiah is a fucking villain. You said it yourself. She's forced the player to ally with Izuka, of all people. She forces the player to murder the same Laguz the player's grown to love in Path of Radiance. She uses murderous, dirty tactics and fights for the wrong side of the war.
But that's not the bad part. It's good writing, and could serve to show a flawed ruler forced into harsh decisions, for the sake of country and people.
But not here. Because of the Blood Pact.
The Blood Pact essentially means that Micaiah is free of all guilt from her actions, because it wasn't actually HER who pulled all the evil shit. She was actually MAGICALLY OBLIGATED by the REAL bad guys to do her bidding. So she is free of all consequences or guilt. Micaiah is free to be the Queen of Daein!
Yeah.
Micaiah is a piece of trash that shouldn't exist.