I've also had this issue, and decided to build a different solution: Toggle Buttons.
![alt text][1]
It provides a better overview over the flags set but takes up more space in the Editor. You can check it out here:
http://www.sharkbombs.com/2015/02/17/unity-editor-enum-flags-as-toggle-buttons/
[1]: http://www.sharkbombs.com/wp-content/uploads/2015/02/ToggleButtonFlags.gif
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