Just to make jumping from sector to sector easier, why don't we have a command line where you type, for example, /navigate "M-14", which would then plot the route into your nav system without you having to divert your attention from the game?

Ooo, good idea!
I propose the command /navroute with the following syntax:
/navroute add "System A-1" to avoid ambiguities with which system you want to go to
/navroute clear to clear the route
/navroute undo to undu an errant add
/navroute list to list any saved routes
/navroute save "filename" to save a route
/navroute load "filename" to load a route

/navroute isn't listed in the console commands section of the manual, so a new player probably wouldn't know about it.

It seems a bunch of other commands are missing too...

-100000 so instead of looking at nav map, you want to type it in while flying and hope you typed it in right

I suspect what is being hinted at is there are at least two plug-ins that already provide this.....and the Devs are a bit busy....

/navroute isn't a plugin. It's already part of the game.