I like the change. More specials, better balance.
Yes, they could've mapped the transformation to a taunt... but there are some issues that would still remain, as seen below.
Transformation characters are inherently hard to balance, because they give you more options. Making it too easy to transform would make them very good as you'd switch quickly to edgeguard with the better one for that, switch quickly for KO power, etc. They'd have to make them both worse, or even out their abilities in order to prevent them from being broken. But the two of them are supposed to play so differently that this would be hard to do. It would be possible, and basically if they went the high flexibility route (very quick transformation) they'd have to make them both just ok on their own, and necessitate that competitive players master both. Some people might like that, but most players evidently don't.
On the other hand, if the transformation is too time consuming to do (as it is in Brawl and Melee), then you can only switch while your opponent has been knocked far away or KO'd, you can't do it on the fly to gain advantage since you'll be too vulnerable. In this case, people will tend to never transform and thus you might as well make them separate characters.
On the whole, as seen in both Melee and Brawl, the combination of Zelda and Sheik barely does any better competitively than Zelda or Sheik alone (Sheik alone, since she's better in both games, as it turns out). The flexibility basically gains you nothing because it's too time consuming to switch.
Making them separate means they get new moves and they can each be balanced on their own. I'm way more excited for both Zelda and Sheik than I was before, because they both look like they'll have all sorts of new aspects to playing as them.
