Muslims neglected? How about orthodox ones? They don't even get bishops(ok thats a bug, but still). You can't even join jihads or crusades with em. However you can be a target for crusades or jihads. You have very small chance to get relics(only catholic ones I think). And most annoying thing is that theres only two orthodox factions. So that means a lot imams and priests on your land praying against you.

And for muslims, yes whole game is unfortunately concentrated nearly only on catholics factions. For example most of special retinue units are catholics only and imams don't get as much retinue as catholic priest. Don't know if they are even finished some factions. For example other than catholic factions have some serious probs with swordsmith guild.