Honestly, if this game didn't have a porn game side with harem route, and had been a more "classic" visual novel with no Dating Sim side to it, Ella would very likely be the girl the MC would end up with at the end of the game.
Don't get me wrong, whoever reads this, I'm not saying he doesn't pair up well with the others. Not at all. But as Drako pointed, there's a very particular connection between her and the MC. They are kin on a lot of points. So that makes it feel like they'd be the ones to end up together.
Permanently, very, very unlikely. Probably clearly not gonna happen, even.
But depending on how the story goes next, "she" could come back more often. For example, if the MC has to go on the run from the authorities instead of being captured and locked up like it's shaping up to be, then his female appearance would be a good way for him to be able to move around, as that form hasn't been outed...