The game play question in abstract terms is how much control the player should have over the civilian traffic. If the answer is total control, then the 'civilian traffic' would simply be another arm of the government/military forces. My concept for civilians is to add some randomness and chaos to the growth of an Empire, which is the opposite of total control. However, you can gain total control in several ways. For example, if you can block civilians from entering specific systems, then you can simply restrict every system except the ones you specifically need. Equally, if you can block specific population as 'military outposts', you can block every population except the one you want civilians to colonize.
I have no problem in conceptual terms with the idea of military-only outposts or military systems, but that mechanic can't simply be a back-door to total military control of civilian traffic. I am open to suggestions on those lines.
I can see your point Steve, I could counter that just about all real world governments, in all periods of history, had military restricted zones where civilians were not allowed no matter what. Personally I think it would make sense, for any kind of possible government, to say that some systems are restricted to government ships only. Obligatory: "You are not allowed to walk into Area 51" joke here.
Ultimately it's a matter of interpretation and game balance. You seem to prefer a "corporate" government, where civilians have very few limitations. Also, you prefer this solution for gameplay balance, in order to "have more chaos"
As a player, I would very much prefer to be able to have more control, not to game the system, but in order to be able to
1) Create military-only colonies and installations (for roleplay!) and
2) Be able to expeditely evacuate a small colony in case of severe threat. Because when enemies are coming, I'd like to be able to tell the civilians to go away right now. Not to see them bringing MORE civilians to a system I KNOW will be invaded in a matter of months
Basically I would like to be able to play with civilians on, while having control in the aforementioned situations. I will also add that as a single player game, ultimately if some players decide to game the system, that's only their problem, not mine.
I do not have any magical solution, I do have a possible one, if you're willing to code it. Once again, a switch.
At game start, allow players to decide whether they want to be able to restrict this civilians behaviour. With this switch off, everything would work as it does now. With this switch on, players would be able to restrict systems and/or forbid planets for migration no matter their size. Maybe with the added caveat that a restricted colony or system has a severe income penalty, 50% or 75%, to simulate the wealth loss/malcontent of the population.
Yes I know, it's ANOTHER switch. It's the only solution I can think of though.