Personally, I think it's a good sign if a plotline or a storyline is highly divisive. If lots of people either love or hate Micaiah, that's better than having a main lord that's bland and boring. And when you have a character that has to make difficult choices, they're always going to be divisive. That's what makes them interesting.
More ink has been spilled over the plot of FE10 than any other FE. What does that mean? That people care about it. That's always a good sign.
I think that for me, the most important thing in Fire Emblem is good villains. FE11 fails for me because the villains are boring. Medeus shows up all of once. Gharnef shows up twice. Compare that to a game like FE10 where the Senators are a constant presence in the narrative.