I'd prefer to see changing governments give more of a bonus, but also more of a penalty. The higher the form of government, the more irritating they can be. For example, federations (the highest form, if memory serves) could have half-yearly votes about various aspects of your team, where they may demand things. For example, after a vote, the Senate could make the demand that you construct more millitary ships for the protection of the empire. This then sets you a goal, where you need to reach a millitary rating of 100 by the time the next vote rolls around, or you have a penalty to morale empire-wide.
There could be a number of demands it could make. E.G.
Set up another two trade routes
Improve relations with a particular race
Remove ships from the boarder of your race and a race you're close to both diplomatically and spatially
Create a millitary starbase in a certain quadrant, with a minimum of four modules
Improve your millitary rating
Go to war with a race that's at war with a close friend of your races.
Research a particular technology
That sort of thing would more then make up for strong economic bonuses provided by your government style. The more bonus' a type of government gives you, the more extreme requests they could make. And if you refuse to meet several requirements they place on you, not only would morale (and perhaps loyalty for obvious reasons, and production, to represent the people not wishing to work hard for someone who ignores them) decrease, but there could be a random event where unsatisfied planets split off into their own minor race.
Long story short: The various government types offers potential for cool gameplay mechanics that I don't think are full exploited.