May I suggest that the jogging controls on the control panel are revamped. Those same controls on the ReplicatorG control panel have a nice little diagram showing X, Y and Z with direction arrows - and it is instantly obvious which direction the build plate (or extruder head) is going to go.
With S3D I am forever choosing the wrong button to lower/raise the Z axis - this invariably leads to the bot physically crashing into its end stops. If the buttons were re-designed so that they showed the actual direction the build plate moves it would help a lot.