The complete and utter inability to come up with a consistent, modern, human-readable, non-arbitrary directory structure comes to mind. People are so blinded by the arbitrarily "designed" [1] FHS they refuse to even entertain the idea that it might just be time to replace it with something better.
EDIT for clarification: layers upon layers upon layers of virtual directory structures don't count. It only adds complexity and makes the system more obtuse.
[1] http://www.osnews.com/story/25556/Understanding_the_bin_sbin...
EDIT for clarification: layers upon layers upon layers of virtual directory structures don't count. It only adds complexity and makes the system more obtuse.