I don't think we need new combat orders too badly, but I would like to see a way to set "default orders" that kick in right after launch. I'd also like for orders to be sticky when switching modes, so if I've got my ship on "Hold position" while I'm in the fighter, and then I switch back to the mothership briefly, I don't have to repeat the "hold position" order again.
Some non-combat orders would be fun too, like letting the crew mine or pick up materials while you play defense in the fighter.
Overall I really really hope the NPC crew aspects of the game get more love and development, so much good stuff that can be done!
Oh, and yes it would be nice to have the switch time be faster and more consistent. I usually deploy the fighter with crew and then switch after, it seems to result in less blind time overall.