Right. Thanks for the clarification.
To the degree that the game was only a Wagon Train in Space prior to 0.9, there are many of us that couldn't wait for some permanency. Colonies created not only a lasting footprint but also removed the "My fleet composition is an end unto itself" phenomenon that existed. (I'm just pointing out the psychology of players going into 0.9)
But, you're right: there isn't an alternative to not having Colonies. Or to put it another way, the majority of the mid-game content revolves around utilizing/upgrading at least one and, if you don't, Nanoforges, Cores, Blueprints, etc. are just rarer commodities rather than anything meaningful. You don't really interact with the new economy system and many of the late mid-game threats (expeditions, pirate/pather bases) never come into play.
So if I'm hearing this right, the suggestion is to have the option to eschew colonies and align yourself with the powers-that-be (whether temporarily or permanently) and therefore have access to the same mid-game content, though at the cost of being at the beck-and-call of one of the factions. With the new Contact system, I think this could work quite well. You would have some superior within the faction that gives you missions, sends you on expeditions (or defends against them), and it would allow you to further the aims of the given faction via dropping loot off with them. Of course, this necessarily puts you at odds with rival factions. Perhaps you stay with that faction forever, "buy" your contract out or, with enough honorable service, you're given a sizable blessing to go off and do your own thing (with a non-compete clause, of course!)
Something like this idea was brought up quite a bit when colonies were first announced, i.e., can you set up an outpost for other factions that you have a commission with (along with the question as to whether or not the factions would expand). At the time, Alex said this was not the case (and still isn't, AFAIK). But back to what I said previously, my hunch is that fleshing out faction warfare is at least another patch away at the earliest because the priority is end-game content. However, I do want to see a more robust faction dynamic, much along the lines you suggested.