I've been hitting this same wall. Driving me nuts. However, there is not limitation on the exact capacity, at least for colony modules. It can b a capacity of 500 million people, or 1 million. I've actually gone the other way. Since it is obscenely impossible to fit so many people into such a small space, I've scaled it down to something more believable, though just barely. My idea was 10million per module. Then a 2nd module at 25 million. Then a 3rd module at 60 million, etc. Keeping in mind that you're really looking less at a colony ship and more at world ships w those numbers. The space and facility requirements to handle even 1million people is nearly unfathomable.
I would say upgrading the system to allow multiple levels of colony and troop modules would be terrific. How does one petition for such an alteration? Also, I use and reuse colony ships to transport populace from a primary world to colony worlds. Just transporting the ship back and forth and back and forth. Its a bit mentally laborsome to keep track, but its a significant advantage. 10 million out, 1 million back, 10 million out, 1 million back. The more modules on the ship, the more efficient the colonization process becomes.
Why couldn't a colony train be built into the system? Like Trade routes. Once a colony is established, send a 2nd colonizer to the world, as per normal. But the computer asks you if you'd like to make a colonial convoy. If so, the vessel ferries back and forth, until cancelled. Each run would transfer x amount of colonists, and realistically consume some amount of resources as well. Ones homeworld could have potentially dozens of convoys running at any time. And you'd really only need to get the colony on its feet, 1 billion people or so, before you retask the given ship.
This is what I do manually, it'd b nice if I could get the computer to do it for me. I wouldn't even mind if it consumed a logistics per route to automate it. It'd b well worth it. Just get your homeworld up to a good level, and begin the exodus to new worlds. At any given time, I'll have 6 to 10 ships ferrying colonists to established colony worlds. Maaaajor benefit to my economy and production; especially since my maxed worlds are losing their pop.growth at max anyway. May as well permanently export the overflow of citizens!
I would love a reply, to myself or the threads. I havn't seen any action on this game in ages and would love to work things out w my fellow civver.