Oh, it's less the what, but more the details of the how as in how to control the colony and how much influence the player has on them.
Well, some ideas to hit you with:
- Players just drop off colonists on a planet that meets certain conditions (breathable atmosphere, temp range, etc
- As time passes, players receive requests for supplies. Planet A (which the player helped colonize) sends a radio message saying "We need 400 crates of food, we'll pay 30cr/crate" or "We need 25 barrels of water and 50 crates of construction materials. Payment of 3200cr upon delivery" or even "Pick up 10 colonists from Station A and bring them here for 5100cr", "Come here and kill these annoying natives, we'll pay 200cr a head", etc.
- You don't own the colony or control it in any way. You're still just a freelancer but now you have a bit more running around to do. Of course, throw in a couple AI transports that do this as well and you can still receive jobs (and you'll have competition). However, if you don't keep up with the colonies they may stagnate or die out. While this won't affect you too badly (after all, you'd just end up where we are now) it might be more beneficial to help them out.
- Colonies grow in two areas: population and infrastructure (both integers). When you scan a planet you see the data (e.g. 12 citizens, 22 of 100 infrastructure). At certain points of pop and infrastructure the planet gains new services, but also has increased demands (bringing more incentive to help them grow). For example, a planet with at least 20 citizens and 30/100 infrastructure may build a landing pad that allows for refueling. 30 citizens and 50/100 infrastructure brings in repair pad and munitions depot. 100 citizens and 100 infrastructure and the planet is as set up as (or better than) a station.
- Maybe down the line colonists will expand their requirements to allow for slightly dangerous planets (thin atmosphere, high/low temp, etc) and will slowly terraform.
There's all kinds of things that can be done that make it seem more complicated than it is.
As for other features not related to colonization:
- Deployable rovers that you just dump on a planet and leave for a time. While gone they slowly explore the surface and gather materials present. Come back to pick them up and you download the data/retrieve the minerals. (If satellites do this please disregard. I haven't used them yet...)
- Stellar anomalies such as black holes (pulls a ship in if too close, but is surrounded by valuable materials), single/multiple use wormholes (shoots your ship across the sector, permanent wormholes would be better because of fuel use and death if you get stranded), and large inter-solar dead planets that do not orbit a star but instead travel on a path through the sector (completely dark so you'll need lights to see, COVERED in valuable materials but extremely dangerous to stay on for too long)
- Nano plagues. A planet being slowly consumed by a Von Neumann swarm that eats away at the surface. Make it a special planet or make the swarm move from planet to planet leaving a trail of barren rock worlds. Only by destroying the hub (while it is in space, of course) can you stop it. Would make an awesome danger to colonized planets or even stations. (Which brings up another missions the colonists can give: Stop oncoming dangerous event like asteroid or pirate fleet, etc)
- Multiple corporations which might recruit your for a contracted period (30 turns, etc). Different corporations give different missions and different benefits. Joining a mercenary wing can give you access to special weapons, exploration corp (Interplanetary Expeditions, anyone?) gives you better engines, etc. Each corp gives access to special hulls as well
- As mentioned above, terraforming is always welcomed. And it doesn't have to be friendly terraforming. Planet A hate Planet B? Maybe they have you drop off the "Atmospheric De-Oxygenator" that slowly drains away the atmosphere until everyone dies and the planet becomes barren, all with the payment of 15000cr directly to your account. This of course brings about...
- Reputation. Do good things you get a positive reputation and vice versa. If you show that you're willing to genocide a whole planet for big money the more "moral" of the groups might not want to do business with you. Hell, even the bad guys might steer clear. Ideally, it wouldn't be the class 1D good<-->bad scale, but would instead be 2D: left and right are Amoral<-->Ethical (or Evil and Good). Up and down are Loyal<--->Ruthless(Lawful and Chaotic, whatever). This might warrant a bit more discussion below...
Let's say a player receives that mission to drop the terraformer on Planet B for 15000cr. Planet B gets wind of this and offers you 25000cr to turn around and drop it on Planet A. And let's say that an arbitrary number is assigned as a "danger rating" for this mission, let's say 12 (with 20 being the highest). If you accept either you receive a shift in the Amoral direction. If you betray Planet A you get points towards Ruthless. If you turn down Planet B after accepting A's you get points towards Loyal because you didn't betray that first group. If you turn down Planet A's mission, giving the reason of "I don't genocide" you get points towards Ethical. If you turn it down because of the danger you get points towards Ruthless.
Now, pirates would have no problem working with a person who is completely amoral. In fact, they might seek you out. A disloyal person, however, they'd feel iffy about working with. Why trust somebody that will just sell you out to a higher bid? A person who is completely Ruthless and Amoral would be ultimately self-centered. Ultra-capitalist. Has a library of every Ayn Rand book. Does what benefits only him(or her) self. A person who is all the way Ethical and Loyal is the ultimate Paragon of Justice. Hunts down pirates without mercy and destroys all those that threaten/go against their ideal of good. This is your Judge Dredd, killing "criminals" without a thought because the law must be enforced no matter the casualties.
Neither of these sides is "good" or "evil". A completely selfish person might never do anything that can be considered "evil". A Ethical/Loyal player can have killed off entire planets if the cause is considered just (you must wipe out the alien scum that threaten our peace!), while the Ruthless/Amoral player would have turned the job down (Amoral = "Your faction warfare does not concern me").
To encourage the player to work towards different ratings and actually care, give each quadrant of the 2D axis a specific faction. And, make those faction opposites at war (quadrant I is at war with quadrant III but on uneasy terms with quadrants II and IV). Corporations would, of course, lie along either neutral axis.
I think all of these ideas emphasize the "freelancer" feel of the game. Not sure if that's your goal or if you'd rather take it in more of a space management direction, but to me running a colony seems too... fixated for this game. Give the player a sense of character, make them mean something other than just a name and a bank account. Even give the crew a sense of character by giving them (fixed) alignments which influence who you hire.
Hell, throw in import/export of characters so you can start a game with an old (even revived) character that is essentially a new player but with your existing alignment (so you can start the game Ruthless or whatever). Not allowing revival even makes player deaths all the more epic, e.g. your character that you've won with six times over is finally killed at the age of 42 after being betrayed by his gunnery officer.
As usual though I have to end this post with a "keep up the awesome work"!