A continue current path key/button would be brilliant, especially in those fleet and freighter moving times (i hate having to constantly zoom out and zoom in just to see the end of the autopath). So i third/forth/fifth that one
Another thing i would like to see is a little manager that would allow you to group planets because in the larger maps sorting all the ships to be constructed and the focus and the building upgrades etc. takes a lot of time (even with the colony manager) and will only really apply to planets near an event etc. (some quick cheap fighters in the 'group' closest to an invasion and some big counter-attack monoliths in those further away).
But on the whole i like the way most of the commands are set out, although a feature to re-bind would be brilliant (especially when you have programmable buttons on your keyboard)