Re: Diplomacy, limited wars, etc...
 

We could use a global badboy penalty for genocide.

In the meantime, I advocate setting:
Number Of Ground Combat Turns := 2
and
Planet Value Percent Loss After Owner Death := 40

With 2 GC turns per month, your ground pounders will be slogging around, slugging it out for years before taking a homeworld. Plenty of time to clear the skies and add reinforcements from both sides, for Troop-Vs-Troop action!
Emotionless races will be able to build defense troops the whole time, so they might actually be worth the 3000 points!

With a 40% loss (or even higher if you like), a nuke-em-to-glass policy will leave you with a barren, desolate starsystem even if you win.
Value-Improved Homesystems can be very valuable indeed!

Re: Diplomacy, limited wars, etc...
 

Yes, the "bad boy" idea seems the easiest one to implement in the game. It would add to anger variable and would decrease over time (slowly). It could be used to penalize all kinds of atrocious behaviors like using plague bombs, declaring wars, breaking treaties, glassing planets, etc.