Some random thoughts on commands...
Concentrate Fire - This command offers a single dice to any ship regardless of size. This makes it a more efficient choice for cheaper Ships (i.e. herd of Corvettes) while a VSD with a 6 dice frontal battery will not notice the effect as much.
Engineering - The value of this command scales with Engineering. Seems obvious but it becomes a more efficient choice for larger ships as opposed to the Corvette with a meager engineering of 2.
Squadron - This one is interesting due to the fact that the token is much less effective (only activate a single squadron) than the actual command. This makes it a more high risk option to set this command on your dial as if you come to use it and all your squadrons are engaged or out of range then saving the token doesn't do much for you. As such you may want to consider providing a 'carrier' style ship some way to change their commands - particularly the Command 3 ships as it is sometimes difficult to know if you will need a squadron command in two turns time or not...
Anyhow just thought that was interesting. It is a gross generalization but expect smaller ships to concentrate fire, larger ships to favour engineering, while squadron commands require careful consideration to avoid wastage. Navigation I find is just really good all the time - frequently more valuable than either a concentrate fire (if you can bring two arcs onto a single target) or an engineering command (if you can avoid an additional enemy arc).
I'd also suggest that Leia on a Corvette should be a default choice for any rebel fleet for emergency commands. Being able to throw a crucial navigate or squadron activation onto an assault frigate can swing the game.