SuperRad: Because you can use them independently and is the most common practice. Although I believe she's a better character if you use her in her entirety (but still, it's completely up to the player if they want to use only Zelda or only Sheik). While I see that as a legitimate reason, what I see as more likely was that the SBR probably -understandably- considered Zelda and Sheik as separate, and if they didn't, still recognized that they could be used independently and so separated them. But if it was common practice for people to actually use both, who knows, maybe there would be a character listed as 'Zelda/Sheik' on the tier list too. But obviously that would never happen since it is in fact so uncommon.
The abovementioned fact that they can be used seperately is why Zelda is allowed in LTT, because Zelda by herself is bottom tier. And one of the points of a low tier tournament is being able to use weaker characters in tournament that you otherwise wouldn't likely be able to. Whereas on the other hand, Singles, Doubles, MM, & Crew Battles are all "all out" kinds of situations, in which you are (or at least most people usually) going 100%, and should be using all abilities at your disposal, all aspects, potential, & capabilities that you have the know how to use effectively with your character. And Zelda is part of Sheik's potential & capabilities and vice versa. Just like desynching to utilize Nana (a "hidden" aspect), Zelda/Sheik transforming is to utilize another part of herself.
Okay, so i've addressed the topic of why they're listed seperately on the tier list, why Zelda has entrance to Low Tier Tournament, and uncessfully conveyed why you should be able to use both Zelda & Sheik together for anything outside Low Tier... The MOST COMMON argument against being able to change (from noobs and experienced players alike) is that it messes up counterpics. This, to say it bluntly, is the fault of the counterpicker, by assuming that the two aren't going to or shouldn't both play a part in the fight and that only one will/should be used. This seems to me to be brought on by a naive, pre-programmed set of laws & ideals of what they think things should be like or what's fair, and an expect others to instinctively follow them. (But why should that group of people be the ones to decide the matter? They're not even the ones who play the character in question.) I see this naive perception of cheapness as a result of the combination of something for the most part unprecedented (the transform mechanic) along with something unfamiliar (the application of somebody actually readily using it in combat). It's new, and some consider it 'too good' or "cheap". There is a fear or concern of a new application they think is cheap, and a want to do away with it instead of learn what to do against it, a feeling of the like that shouldn't exist in high levels of play. For, as good players, you should know that many 'good' tactics/strategies (if you want to call this that), when first discovered or used are often regarded as "cheap". But that should never stop the developement and progression of what's possible. In a healthy metagame: good technique begets a countering good technique, counters beget counters, and what is considered cheap one day is wholesome and fair the next. That's what progression is all about; if you deny the use of something, it only denys your own potential, for you will never develope the strength to fight it or gain what was learned along the path for that strength, and will forever live in the dark. There is almost nothing in this game that's so good that it's banned. The progression i'm aiming for here today is more of an understanding and realization that, in a simple way of putting it: Zelda is to Sheik as Marth's Fair is to Marth. Zelda is an integrable extension and in some cases a compliment to Sheik's game. I would guess I use her around 20-30% of the total time of all matches (figuring both: fights that I use one or the other in, and fights that I use both in (I would use her more, but she's still only bottom tier by herself)), imagine taking away such a large percent of her game. It's like a Falco that's told "From now on you're only allowed to use your neutral-b half as much as you have been."
Rather than considering Zelda and Sheik as seperate characters, of which the opponent will chose one and stick to, instead they should regard them as two parts to an ultimate whole, and recognize the threats each has to offer and go from there (they can also consider who they're fighting against to further evaluate the specific threats they'll be facing) . The only argument I see against what i'm saying is people maybe then thinking Zelda/Sheik is unfair because she would be good against too many characters. But consider who sheik is 'good against', then factor in how many extra match-ups Zelda contributes to Zelda/Sheik as a whole, and you end up looking at a number that's right there with the average number of the other top/high tier characters. So how much good does that really do? Does it really make that much of a difference?
And Delphiki, I don't see it as a issue of semantics.
Personally, I don't see why most people have a problem with it anyway. The combination doesn't contribute a whole lot, and then when the possibility does arise, it's only useful if the player in fact knows how to use both of them effectively anyway, and most people don't utilize her entirety, so it matters even less. Attempting to ban one of them seems to me to be a convenience from people who don't care to think that maybe they really can be two parts of a whole. I'm not saying that they can't be used independently, only that you should NOT always think of Zelda/Sheik as seperate, think of them as a potential single entity opponent/teammate!