I considered a new thread since this is a pretty long string of mostly interconnected ideas, but I figure it can always be split later.
I put forward the possibility of a generic "happiness" system, where each colony has a "happiness" associated with it. Things like government type, occupation, environmental effects, etc. cause negative happiness, while other things such as, say, lower tax rates (will talk about later), certain new technologies, amount of trade and the like cause positive happiness. An advantage to this is greater flexibility and depth, such as conquering an enemy planet and bombarding them with luxuries, which makes them think that perhaps their new government is better then the old and integrate into your empire faster, or even a planet that's wealthy enough, with enough trade, that most people don't care that they've run out of available infrastructure and the lower-classes are dying in droves. A lot of the things that right now directly cause unrest would instead cause unhappiness, which in turn, if negative, causes unrest proportional to how unhappy people are. In the same situation nothing should change, but it provides a better alternative to "shoot everything that argues".
Another part is a greater depth to the tax system. Total wealth generation becomes much higher, but you've got to balance "civilian" funds and the "military" funds (in this example, military funding is what we're using right now in Aurora). There's a slider somewhere, probably in the race details screen, that determines what percentage goes to each. More civilian funds would make the populace happier, while more military funding would obviously help a lot in a pinch. Individual colonies could also have their own sliders that default to whatever the empire-wide tax rate is, with, say, a check box specifying that you want to manually set it for that individual colony.
Together, and assuming happiness has some positives (such as higher population growth, perhaps more civilian trade goods produced, etc.), I could see things like lower tax rates in peacetime to expand swifter, and then drastically higher rates in war which make the population angrier the longer they stay high. Or, much more fun, conquering a planet and taxing the population to the maximum as reparations while keeping them in check with ground troops.
EDIT: Another suggestion: A new tech line called something like "Hyperdrive Stability Factor" or whatever, but it decreases the effective radius of the hyper limit for the hyperdrive.
