Microsoft and Apple as leader dropped the ball. Microsoft's several dozen Windows-related teams dont care about UX (maybe UI). Apple is busy making money and mobile.
It really is currently the time and chance for Linux to finally innovate again.
* Alternatives to tree filesystem UNIX introduced (see WinFS, or how Android/iphone manage it)
* Alterantives to WIMP as discussed, specially for large monitors (37" - like 57")
* Every App should provide a REST API to access its functionality remotely (for AI and data exchange. Think OLE/COM in Windows, but good)
* PLAN9 anyone?