There are other ways to deal with this. If, for example, there are circumstances that give the player great bargaining power. And it just so happens the player DOES have something to bargain with - blueprints.
Given the state of the sector, the idea that all major powers would want an edge is a no brainer. But exploring old ruins and space in general is dangerous. Hence the idea of bold explorers being given extra rights and even access to some better hardware (still not top capitals), because remnants. For those that know 40K, think Rouge Traders. Basically, the player would be one of those individuals with the rare right to have some military-grade ships in his fleet. And the more you prove your worth by bringing in blueprints, scrap and helping out a faction, the more hardware you get access to.
Thus, when you inevitably find lots of blueprints, you can sell them to a faction and in return of not just the tiny amount of money you get (because the value of these things should be insane), but also the first ship/ x weapons produced by the sold blueprint.
After all, you have bargaining power - you can sell it to their enemies. Speaking of which, selling blueprints to an enemy faction should have consequences, depending on blueprint.
I'll have to be honest and say that I never liked the idea of the player creating his own empire completely independantly - not in SS at least. While a great idea it just doesn't seem to fit in the universe/scope. Hence, I see nothing wrong with commissions or some kind of permanent commitment being REQUIRED not only for the player to get the good stuff, but for the player to SURVIVE.
In a hostile and militarized universe, with the player sorounded by giants, him creating his own empire and doing whatever he wants just feels wrong. If SS was a movie, the player would be the Ultimate May Sue. Note, I'm not against the player being able to create his own faction, but it's the way it is done that bothers me. You should NEED a protection of a bigger fish in the early stages. Starting off as a vassal of a sort, with the early colonization and defense being helped by your patron faction - for a cost of course. Your colony would be expected to pay tithes. Then later, when you get sufficiently strong, you can declare independance.