The problem with thinking this way, is that it's not how Sakurai thinks, which means you're going to be wrong. You can believe whatever you want about what would make Smash better, but if you're trying to actually PREDICT what will happen, the only way is to is interpret what Sakurai has done in previous games and what he has said to try and understand HOW HE THINKS.
You're looking at it from a competitive viewpoint, which Sakurai obviously does not hold. He's said a few things about what he thinks balance is and how he goes about doing it, and how from what he can tell everyone is balanced well enough. There is no indication whatsoever that he would feel Zelda and Sheik would need to be changed so drastically because of balancing issues. If anything it would be on the contrary. I guarantee you if they do get separated Sakurai would not cite that as the reason why. Not to mention the amount of people who actually complain about it is negligible (and they tend to have bad ideas anyhow).
I mean, if THEEEY had their way they'd remove anything charming from the game. "Oh, Pokemon Trainer's stamina thing isn't executed as well as I would like it to be, better separate them. The Ice Climbers can create infinite combos, so it would probably be best to have only one out on the stage. Pikmin are so random it would be best to pull out a certain one depending on the attack since some provide better effects than others making the rest useless. Lucario's aura mechanic BLAH BLAH. After all, it's for gameplay reasons."