First off, Melee was unbalanced as it was, I really doubt Sakurai would've boosted Zelda if Sheik was cut. It really doesn't make any sense in a game where the tiers of all the characters vary so much.
I still fail to see how having Sheik cut would increase the usage of Zelda, considering they didn't like using Zelda when Sheik was around, why would they like her if Sheik wasn't there? They would have gone off to main someone else like Fox or Peach or what have you.
You're can't be seriously saying that they'd cut away half the character that was Zelda/Sheik and leave Zelda in what awful state she appeared in Melee? Also I said that if Sheik was a limited transformation of Zelda then Zelda would actually be played more (also true if her moveset was greatly strengthened), which is true because people that wanted to use the awesome character that is Sheik would learn how to use Zelda effectively to transform to Sheik.
Second, we are not even talking about how good ZeroSSamus is, it's not the point! It doesn't matter if Samus is stronger than ZeroSSamus or not, pretty much for the aforementioned reasons. Even if ZeroSSamus is the worst character in the game, there will be times when someone wants to play as her, and guess what, you can't! You have to pick Samus, wait for a Smash Ball to appear, AND make sure you get it and not one of the other one, two, or three characters on the map gets it first. Under these conditions, you'd be lucky to have ZeroSSamus for even half the match!
ZSS was never stated to be a pure character addition. If people want to play solely as ZSS then they're missing the point of the whole transformation business. If ZSS was never intended to be included to be played as a character in her own right, then any expectations of playing ZSS individually from Samus are misfounded and to be honest a bit greedy. Her strength may or may not matter in how much she gets played (as there will always be those that play characters despite how good they are) but I was just pointing out that in either case of extremes that limited exposure of the character would be beneficial for the sake of balance.
Point number 2 would be that looking at it from the side of people that never want to play as ZSS, they limit themselves to never using Samus' final smash attack. While I admit this is much easier than playing as ZSS via transformation, it still gimps a player's abilities while final smashes are on. However the point of the move and transformation is that ZSS and Samus are linked, so if you want to play as ZSS you need to use Samus to do it or if you want to use Samus' FS then you (potentially) have to pay the price of using ZSS for <insert period of time>.
Third, this isn't even counting the items discussion. You are literally restricting an entire character just because you turned off items. If you are fine with this, you don't appreciate the resources spent on making a character in such a game. Even bottom tier characters in Melee weren't physically restricted, they were always there to be used, just chosen not to, whereas you would actually not be able to use ZeroSSamus whether you wanted to or not.
At the end of the day, the VAST majority of people playing Smash Bros. will be playing with items on, albeit maybe with certain items turned off, and the minority that chooses to play with all items off, included the FSball, have only themselves to hold responsible for not being able to play as ZSS. On the point of resources, the inclusion of ZSS as a pure addition character adds in more Metroid representation without taking up a character slot, adds variety to Samus' moveset, sex appeal and increases the number of female characters. Hardly a waste of resources or time.
Summary:
If you still think it is worthwhile having a character who can be used, on average, half the time, instead of a character who can be used all the time--whenever and for however long you desire--than there's nothing left to discuss, you just can't comprehend things on a comparative level, and don't understand efficiency and "time well spent."
You're right, why should they even bother trying to implement things which add depth, strategy and uniqueness to the game, surely that's just a waste.