Some features I would love to see:
Free-form targeting
"Target select" specific orbits and orbital keyholes
Destination targeting on map surfaces
Airport landing HUD
Destination points on maps (i.e.: KSC and airports)
The ability to construct space centers on other planetary bodies
The ability to construct mass accelerators and rail lines (mass driver, railroads, and maglevs)
Spacecraft component simulators (launches, re-entry, takeoffs, approaches, vacuum, etc.)