Tagging - I was so excited to see this introduced in the new Mac OS! It just makes sense to bring it to iOS. For years people have been complaining about the lack of a file system, here is the perfect way to replace it. I'm honestly surprised that it wasn't included.
Lyrics on iPad - there is no good reason why this was removed, put them back.
Colour changes - this is a small thing, but it bugs me. I don't like the colour white, no reason, I'm just not a fan. I don't own any white furniture, I only own one white shirt. I don't mind the new clean look, but hate the colour. They mentioned that your choice of wallpaper would change things system wide, could a blue wallpaper give white apps a tint. I'm not asking for major customisation, just anything but glaring white.
A few years ago when I first got my iPad 1, I made a list of everything I wanted. I've been slowly crossing off items from that list, now the only items left are tagging, smart albums in iPhoto an app to create epubs (which is probably on the App Store by now).