Custom sounds in general: Everything should be able to be edited.
Themes as people have stated.
Higher build quality. Returning phones due to this is stupid. As well, a metal back again.
Ability to use phone as storage device w/o using a 3rd party app.
Ability to kill processes from the OS directly.
FLASH (this can be done now, WTF)
Better battery life & user replaceable.
And finally:
Apple providing replacement parts that can be purchased online or at the Apple store. Scratched screen? Replace JUST that. Case is worn, replace it. Bezel nicked, replace it, ETC. Apple would make more money if people could walk in and do that instead of getting an entirely new phone, especially if they sold the items for not too much above cost. More people would end up actually spending the money to replace it. I know I would.