Why not go the Cho'Gall route?

One player picks one of the characters and the other becomes available for their whole team, regardless of ownership. They're always played together, never separate.

I understand that somewhat limits the character, since you're less likely to play them, but as it stands, how do you balance the character? Either you balance around the bonuses being there are you balance around them not being there. If you balance around one being played without the other, then together, they're too strong. If you balance around them being together, then nobody will play them separately anyways since they'll be weak. Or you meet somewhere in the middle, and while it's not as pronounced, they're both a little too strong and a little too weak given the situation.

When you have characters that have synergies and strengths decided out of game, that's just how it works out. There's really not a way around it.

So you balance around them being a unit, and make it so they're always so. And Cho'Gall's super fun to play, so who's to say this wouldn't be a lot of fun?