I would love to see wordpress have a easy and simple built in navigation. Instead of Display by pages, or display by link categories. How about fully customizable fields? I would love to have that.
Insert name of link in one box, and insert URL in the other box, no digging through the code.
Same with styling. Insert nav background Here, Insert Mouse Over Background here. and so on.
by the time you got a site the way you want it, you've got 20 plugins installed lol.