1. I don't think there is much point in this, as only the Auri seem to even have enough of a height difference. Rather I'd take have an age-slider that 'scales' the face, height, bust/shoulders and butt by a small factor (eg "young, adult, battle-worn, elderly") to at least give some reason for the shape difference, particularly the face.
2. Muscle tone slider , aka "thinness/fatness" I think is within the reason, since most of what accounts for fatness/muscle tone in a 3D model is increasing the diameter of the body parts by some scale, which would also scale the gear they are wearing. Why it wouldn't work the way we think it does has more to do with the clipping of loose fabrics when the character emotes.
3. That is certainly needed.
The Miqo'te tails I've always had a love/hate with. They don't move like cat's tails, but seem too articulated in emotes. Like to give you an idea, when you move about, it's like the tip of the tail is being pulled up by an invisible string, and is more like a sock than a tail. I'll buy that it's only cat-like in appearance, but it makes me think that when they went from V1.0 to V2.0 they just didn't give a damn about how tails work with clothing and let it clip through everything instead of having gear take tails into account. A similar point can made about Auri.
So if you add new Tail shapes, it probably wouldn't work just from not being able to use the existing Miqo'te tail shape in animations. Likewise with the Ear shapes, some clothing, particularly robes have "ear socks" so changing the shape of the ears wouldn't be doable.
I've thought of reasons for why the face and the horns on an Au Ra aren't separate and I think it's likely the face and horns are fused for conversation animations. It doesn't really seem like it would be much effort to separate them as the horns are all attached at the same point, but it might skew all the "hat/helmet" gear.
And again... butts. While not really a big deal to me, you can clearly tell which gear was from V1.0 because of the larger butt and tail allowances.