Package manager that controls the entire system, not just add ons.
Choice of desktop environments, no silly $3 apps to enable simple things like edge snapping. Options for tile based window manager, etc.
Decent cut/paste (no control-v and control-c instead of sweep and click to paste).
SystemTap for performance analysis.
Seamless use of containers with the same environment as the host OS.
Ability to create binaries that don't require the approval of some Apple run web service to run.