mods are a great way to not only enjoy the game but to add what you as a person are actually looking for rather than feeling with any settlement issues. as for naming ships and planets you can do that atm by clicking the middle lower icon when you have it selceted but this is limited to cap ships starbases and planets

Its easy to make a mod that just changes the names of planets and ships, just go to the string file and look for planet and star names and ships names and just change them to what you want(you can also change Player AI names if you want)

hope this helps.