This is what he got for me
Alright, the answer is still a little fuzzy, but so far I am leaning towards Seamus as my official answer (and not just because you have the Mad Hatter in you list of favorite characters).
In both series, the first character that you mention is the main character. There isn't a lot in common with either of them, aside from their status as main characters. They are both central to the events of the story, and no one can argue Seamus isn't central to the stuff going on. They both have big impacts on the world around them, and Seamus is the most wanted man in Malifaux. They are also both on journeys. Really, that is what both Kingdom Hearts and the AMA games are about: wading through metaphors to find out some kind of truth. There is no master in the game that moves like Seamus does. You get to choose where and when to approach from, which makes every game the story you want to try and write.
Seamus isn't a protagonist, but it IS Malifaux we're talking about. Truely good people tend to just die faster.
You also mention The Cat and Zexion, which are both manipulative characters. Physical disputes are beneath them, they choose to play smart instead of playing strong. Neither one really wants to take part in conflicts as opposed to manipulating other factors to decide things for them. For every step forward Seamus takes, he also takes a step back after he has made his mark for the turn. No one can engage him unless he wants to be engaged, and he usually doesn't want to be engaged. He is the master of the Belle's crew, and no one controls the board like the Belles do. With a little bit of creative movement and Lures, you can make sure that the enemy is dancing to your tune instead of vice versa.
I'm also taking some liberties considering you have Castiel as an icon. If I had to pick a character whose narrative role feels like playing Seamus does, I couldn't think of a better answer than the Angels from Supernatural.
And his first inclination was neverborn. My favourite factions are Arcanist and Neverborn but I do love Seamus He's really good