ORIGINAL: rosseau
Ryvan,
You probably know this, but you can change the race attributes of the Humans to make them more playable. Of course, this is cheating, and some may be looking for a less artificial means to do so.
My problem with doing that is it would make the humans, (or whatever other race was adjusted in this manner,) too easy at the start of the game. I like the idea of not being able to go hog wild with building everything you want on every planet without consequence. That's why I'm complaining about the bureaucracy issue as opposed to population happiness in general. The happiness penalty for humans stops them from being able to go crazy with mining on rich worlds with bad habitats. It's an interesting and perfectly valid penalty to have.
A hard-to-implement solution would be to have some type of bureaucractic building that lowers the bureaucracy unhappiness hit for a particular planet. These buildings would need to be upgraded as your bureaucracy penalty grows. They should be expensive enough to upgrade that they would serve as a limiting device against uncontrolled expansion. They should only reduce the bureaucracy penalty on the planet on which they are built. They should not increase general happiness outside of the extent that they cancel bureaucracy. (In other words, they wouldn't save you from rioting caused by overpollution of an already bad habitat.)
Another solution would be to have the bureaucracy penalty naturally decrease with time if there is no further increase in the size of the empire. This would also have the effect of limiting the speed of expansion without creating a hard maximum size of an empire. You would be forced to expand at a somewhat controlled rate with pauses to allow your government to settle in for a bit.
An easy and less elegant solution would be to add a "no bureaucracy" switch so players can simply turn it off if they wish. (Call it Galactic Conquest Mode or somesuch.) This would allow players who are happy with the status quo to continue on with the current rules and let those of us who don't like it to change it.