I get that some purchased an S because they couldn't get a 3 at the time but if you remove that segment of the owner group, for the those who purchased an S for the looks and load capacity the 3 isn't a viable alternative.
Similarly, if you start taking design elements from the 3 into the S, you remove what a lot of people like about the S and dislike in the 3.
There is no perfect solution here, but there is nothing wrong with the S reducing in over-all numbers as the 3 ramps up and you'll see something similar when the Y arrives as we;;, both for the S and the 3 as there will be people right now taking a 3 because they can't get a Y yet and can't afford an S...
As for the price difference, check out the Audi A7 vs A3 for example... There is room for the S to command a significant price increase over the 3, just don't make it look like a larger 3/Y