The USE flags thing is a nice way of gentoo to handle things; the list of flags gets longer, it is however still too short, but already uncomfortable to handle. Browsing through the list of flags is hard work, especially since most flags are sparely documented or not at all explained. What I would like to see is a configuration software, that helps selecting the flags. It could be a curses-based GUI, like the kernels 'menuconfig' thingy. There, flags could be selected, the user could get help for each flag easily (even longer help, which currently would make the plain list even harder to read). Flags could be categorized; such as database-, security-, X-, hardware- and whatnot-oriented flags. Flags, which only have any effect when other flags are also used, could be hidden until the other flags are selected; Lots more new flags could be introduced, making the system much more customizable and thus more powerful, which is currently not possible because the list would grow too big. Sorry for the bad description; hope you get the idea anyways.
`emerge ufed`