One person commented asking if the ships will have transport pods. My original answer was no. But on further thought, I realized that it'd be hard to balance if you can instantly create transports and send them off anywhere. If you see an incoming fleet, you can pack up and leave in an instant. Or you can easily colonize every planet in your region by sending 1 pop to each planet.
So I'm thinking of scrapping the "transport ship" idea, and adding transport pods to ships, so it'd require you to have ships to carry people. Each pod takes up a lot of space, and have a limit on how many people it can hold. New technologies will give you new transport pods that can store more people, or reduce the space usage, or other improvements.
Then the artwork originally planned for the transport ship will be your race's "Ultimate" ship (they're 256x256 pixels).
While this may add a bit more management, it'd help balance the game. The starting fleet will consist of two scouts and one transport ship (a large ship that has all the space used for a transport pod). Or if you're a space race, two scouts and two "motherships" that generates output.
Any feedback on this idea? I haven't started on this yet, so would like to hear your opinions before I commit to it.