6.3 is very stable, but 6.4 has a fix that despawns old civilian ships. In my 6.3 game I have a massive amount of civilian shipping, much of it using old tech. 6.4 makes it more likely to decommission outdated civilian shipping.
I'm experimenting with dropping factories and duranium onto my colonies to give the early population something to do, but it seems that the colony generally produces more infrastructure by itself through trade than it does through industry.
It's a good idea to drop some factories on well developed colonies, because they can make spaceports given the proper materials. It's also a good idea to have a commercial ship under your control set to repeat deliver ground force training components orders to those colonies. This is so that you can make some construction brigades which double as political stabilizing ground troops as well as construction points. I use 3 brigades and one garrison brigade on worlds that I'm not going to put a lot of factories on or that are too high a colony cost to employ construction factories.
A good way to do that is to ship all your original GFTF Training components to the Moon once it's settled. Then build one Ground Force Training Facility at Earth and set your commercial ship to repeat GFTF haul missions to your new colony, with refuel earth orders too. It's best done on repeat unless you have a massive cargo ship or fleet. Each standard cargo hold transports .05 of a GFTF. You can haul around the Moon's GFTFs when you want to train a whole division, or the Earth's one GFTF if you only plan on training a single battalion of Garrison or a Construction brigade to keep the planet from stopping work due to low political reliability.
A funny story, in my last 6.3 game I accidently left 'destination of colonists' at Luna turned on. I then went ahead 500 five day turns while I did something else. I came back and over a billion people live on the slightly chilly terraformed moon while only 65 million live on Earth due to my massive civilian shipping lines and spaceports.
I had just started the research prior to those 500 five day turns for genetically modifying Humans into Mercurians. Almost all my scientists were transported away from their Earth labs to Luna in the course of the moon migration.