Yeah I can understand not being able to pull over colonies but that's a small price to pay for being able to transfer almost everything else.
Eh. Use console commands to import some stuff it bothers you to much. Personally I like coming up with settings, to play from. Honestly I kind of roleplay it. Last time I was a the last surviving combat ship of merchant caravan who decided being a pirate wouldn't be so bad so long as he could still kill pirates. The play through I'm on right now I'm literally role playing a person who broke from the ludic path, only to seek commission in the blackrock navy and create a free port empire that slaughters both pirates, heg and pathers a like while bringing back AI ran colonies for better or worse. Yea I'm roleplaying the *** out of this but console commands let you do it and its kind of interesting. I don't make decisions based on what I would do. I make decisions based on the character I'm playing do.
Either that or just start carbon coping your fleet over. Its kind of boring for me honestly. I would also mention that unless your crashing a lot or really need a new feature there is no need to update all the time (inb4 the hammer falls look people if your crashing a lot chances are its means you need and update or to
check your versions). I've got 9 mods that need updating right now according to version checker with a multi colony empire stretching all over the map. Runs fine. I think I've crashed one whole time this campaign to an error I can't seem re create.