I have thought a lot about the problem (worked as a professional bassoon player for a very long time), and I can't say I have had many good ideas. There are some ideas for simplified music notation (with different shapes for flats and sharps) which work _very_ well for making sight reading easier. Until it doesn't: It can't express enharmonics (different ways of writing the same note), which makes tonality analysis harder, and can actually hamper readability since most people that are fluent in reading music usually "stay in key" when reading music.
A quick google gave me this: http://musicnotation.org/ and I can't say I am very impressed by anything I see there. But as you notice, most systems are oriented by lines. I don't think that is because people lack fantasy, but because it is a pretty good way to write music.