It just suddenly came to me in a flash of inspiration; the alignment trees need to be limited in a way. Look at my mock-up of how they are currently;
(I'm a professional artist as you can see)
As it stands, you can select whatever you want from the trees so long as you have the requisite amount of points from random events and stuff, meaning that theoretically, you could have all three ideologies maxed out with no repercussions. This is bad because it means that those that specialize, or otherwise RP their civilizations will be put at an extreme disadvantage for not pursuing all three branches. Specialization should be rewarded, while generalists should be limited in some way to prevent them from out competing them.
In that vein, here's another picture;
Here, I've selected the first tier of "Good" options, and as a direct result, the last tiers of "Neutral" and "Evil" are crossed out and unavailable. In-universe, as my civilization grows more compassionate (or apathetic, or ruthless), the more extreme aspects of the other ideologies begin to conflict with my chosen path, meaning my people won't accept them. In-game, this means that players who generalize when it comes to ideologies can only select lower-level powers and abilities.
Here's more examples;
The second tier of "Good" is selected, and by extension, the other two are now locked-out.
Both the first tier of "Good" and "Evil" have been chosen, locking out neutral and the top-level options for both.
This is the best I can explain it without getting overly-verbose. I feel this would improve how players interact with the alignments in the game, and give incentives both to specialize (To get maximum benefits from a certain path) and generalize (To get more dilute bonuses over several trees). You can extend this over more layers if you wish; it works about the same.
What are your opinions on this?