I think there are two kinds of 'evil' if you will.
One that thinks only of the ruler and makes his life easier at the cost of everything else, even his own population. This kind of evil could result in political instability and even uprisings if your security forces aren't up to the task of keeping dissent down.
The other one (and one that isn't really represented in GalCiv) is being evil at the expense of others but in favour of your own people. Your people is the only thing that matters, all else is secondary.
With regards to the OP, there have been threads about the good-evil debate where it has been more or less established that evil is best with neutral being a good second. A few ideas to rectify this have included boosting the bonus for choosing good or to turn ethical dilemma's into opportunities. This means that every choice gives you a bonus of some sort while still following some ethical alignment.
One idea I just came up with is the following:
Being Good in GalCiv II means you look out for others. You can be trusted and you respect others. Evil nations can be relied on to jump on every sign of weakness to stomp all over you.
So how about giving Good nations a decent diplomatic bonus and Evil nations a penalty? As the game works now, Evil nations like each other (+ for ethical alignment) which, in my opinion shouldn't happen. Evil nations don't just band together unless it is called for by opportunity; these nations can't be trusted.
Good nations on the other hand can be trusted and should build a decent amount of goodwill with other nations of a similar alignment. In the end, Good nations should band together and form alliances based on mutual understanding and trust.
This setup would mean that Good nations on their own may not be as powerful as others but they band together, forming a 'bastion of light' against the cold dark heart of space - if you'll allow me to put this more or less poetically.
In short diplomatic influences regarding ethical alignments should look like this:
Evil nations:
- for other Evil nations
- for other Neutral nations
- for other Good nations
Neutral nations:
- for other Evil nations
+ for other Neutral nations (or maybe nothing)
+ for other Good nations
Good nations:
- for other Evil nations
+ for other Neutral nations (or maybe nothing)
++ for other Good nations (I took ++ because being Good is a tough and conscious choice you make).
In the end, Evil nations end up being alone and diplomatically isolated. Neutral nations have some goodwill (through extra trading for example) and can form friendships. Good nations will band together and work towards a common goal.
Anyway, just an idea.