See arduino/Arduino#3877 for previous discussion.
The problem is that a library is not recompiled when the include list of the main sketch (or of another library) has changed, despite the compilation option (include paths) are modified.

Note that when library-to-library dependencies will be completely supported (#12), i think it will be harder to find a reasonnable case where it is really noticeable. The only one i can think of is the one suggested by matthijskooijman, with the conflicting secondary header files.

I still think however that the proposed solution (each library generates its own dependency list) would make more sense and avoid bad surprises in some corner cases.