Hey. I just asked a question in another thread to Brad/Frogboy in another thread, and I felt it deserved more attention here.
In Galactic Civilizations 2, we had the three alignments as I'm sure most of you are aware; Good/Neutral/Evil. This trichotomy sucked the big one for a variety of reasons, most telling of which was the fact that the good alignment was absolutely terrible. It's easy to pin why this was so; it comes down to three things;
1. Colonization events killed you: Good, as it was called before, or benevolence, as it is currently called, had colonization events that butchered an early-game player, requiring you to take massive hits to industry, research, morale and everything else. In contrast, neutral and evil choices produced incredible benefits in the same areas with virtually no repercussions, giving those players an undue advantage. Players that wanted to be good were almost universally better off choosing assorted evil and neutral choices, then choosing good when you got Xeno Ethics at the end of the colonization rush. Which takes us to point two...
2. Moral choices and doing the right thing was meaningless: It's really difficult to believe your choices are meaningful and have impact when there's a technology that enables you to choose whatever alignment you want with a monetary cost that isn't even particularly bad. So a player who did nothing but slaughter and rape his way across the planets he settled could decide to make his civilization saintly with the click of a button and a low monthly fee 
. This left those who did the right thing high-and-dry, with nothing to show for it.
3. Benefits from being good were minimal: When you got down to it, slogging through all the BS to get to the alignment, the benefits were paltry;
- "Citizens are more loyal and less likely to defect if their colonies are under an opponent's influence" Unfortunately, this meant nothing, it just gives you a few turns of grace when you planet is going to rebel. The "Cut-off" point is still 4.00 X Native.
- "The five most populous planets have no maintenance costs for their initial Colony" Oh Em Gee! This will be so useful in my civilization of 200 planets filled with discovery spheres and industrial sectors! I'm sure my income of 75,000 BC per turn will be greatly improved.
- "Trade income with other good civilizations is increased by 25%" This may actually have been useful if trade wasn't insignificant compared to taxes and (in TA) tourism. This adds at best a few hundred BC/turn on larger galaxies.
- "Gain a Diplomatic Ability bonus when dealing with other good or neutral civilizations" Actually useful! 
- "Unique technologies include Superior Defense" The actual defenses were useless and too expensive for their tech level, and they were swiftly replaced by Aereon Missile Defense, Invulnerability shields and the like. The passive benefits to defense (+10% Defense, +5% HP) were somewhat useful.
- "The "Temple of Righteousness" Galactic Achievement is only available to good civilizations.' Great, so I can steal a small amount of money from others, even though I'm supposed to be benevolent? The bonus is nice in larger games, maybe a few thousand BC/turn, but it's just a drop in the bucket and not really useful.
For changes, I'd...
1. Give 'good' colonization and random event choices an 'intangible' benefit in the form of approval, loyalty, influence, and planet quality etc...
2. Expunge Xeno Ethics and piss on its grave. Make your chosen ideologies permanent.
3. Make the various sub-branches of the ideology trees, not restricted to good, confer more powerful benefits that are in-character and meaningful. Latter upgrades on the tree should also confer penalties to aspects of your empire opposed to your chosen branch.
tl;dr: Make the good alignment not suck and make all ideologies carry irrevocable baggage and penalties to accompany their benefits.
