This thread, this feeling, so much. I was loving this game until I made a colony. I loved every aspect of the early and mid game -- smuggling and bounty hunting and running from big pirate and [redacted] fleets, using and then dumping commissions to get the ships I want, learning which fits and fleets I like, etc.
But now that I have a colony, I'm kind of done with this playthrough (maybe that's the point? get the player to realize the game is over and there's no point playing when your colonies crap out Paragons for you every couple of months?). I've ended more pirate lives than Woodes Rogers and scurvy combined, because with a handful of colonized systems I'm just flying back and forth from pirate base to pather base over and over. It's still an awesome game and the endgame/colonies mechanics just taught me that where I find my fun is in the early/midgame. But once I get a handful of capital ships and can fight off pretty much anything, the only thing left is starting a colony and then playing pirate/pather whackamole and babysitting my colonies protect their precious nanforges/synchrotrons/ai cores from the relentless onslaught of every other faction because I had the gall to mine ore and produce fuel. It kind of breaks immersion -- these guys are dying by the thousands and throwing away tens of millions of credits worth of ships, and never succeeding on a single raid/terrorist attack? Where the heck are they coming from? Why are their leaders throwing away so much? Why not be like, ok, I guess a fleet of death star paragons is a little much for our 10^3 pirate base, let's go back to raiding Nova Maxios again.
I wish more mods went into adding depth/variety to and extending the exploration, salvage, smuggling, and "just scraping by in a rag-tag fleet" feel of early and mid-game. Some kind of Homeworld/BSG mode where there are few markets and the player goes from place to place salvaging what they can, moving on and fleeing from usually-stronger enemy fleets would be awesome. It would also create way more fleet variety by forcing the player into suboptimal fleet/fit choices that I feel like people just bypass right now because money is so easy to come by once you get how smuggling works. I guess I could also just force myself to stick to some kind of theme, like "no colonies" or "low-tech only."