This is an old thread but I'd rather necro than start a new identical thread.
I took a long break from this game, mostly due to hating the colony limit thing, and have been playing again after the Retro update.
But the problem remains for me - I despise the colony limit thing.
It wouldn't be so bad if it was intelligently implemented instead of some blanket thing that doesn't work most of the time. The limit should scale according to game setup - galaxy size, number of AIs, planet quality, etc.
I personally, since GC1, have always setup to play larger sized maps while removing some of the AIs to give more room to expand. But with GC3 and colony limits, it's a constant fight against colony limits. Yes, you can tech around it and eat the morale penalty but it forces you to play a certain way and to pursue the same techs and suffer the same penalties every time you play.
One of the GOOD parts about any good 4X is having flexibility in how you play - something you used to get with GC 1 - 3. And while we still have a plethora of options to setup a game in GC3, the colony limit dramatically impacts whether or not you can fully enjoy some of those options.
In addition to that - no, I don't want commonwealth(s). I wouldn't be playing a game where I could develop a huge empire if I didn't want to manage a huge empire. This is one of the reasons I don't like Stellaris, which constricts you even more. Commonwealth as purely an option would be fine, but commonwealth or suffer penalties is not fully optional.