Upper-case subscripts are missing, for one: I'm not allowed to talk about the normal force F_N in plain text email. Superscript and subscript Greek letters would also be nice to have, eg in context of relativity.
Why not Devanagari then? This Europe-centric point of view bother me.
Sure: As I mentioned in another comment, I'd add markers to enable arbitrary super and subscripting.
However, the question I responded to was asking what specifically people were missing in practice, and the examples I gave are things I personally would have used if they had been available.
Also, I've seen a lot of different symbols as subscripts in mathematical and physical articles, like squares, triangles, arrows, etc.