My general view of what should differentiate the alignments (systematic): Each has an internal and external strength toward an objective. Good: diplomatic (ext), defensive projects (int), goal: form relationships/alliances to build strength in numbers, preventing conquest by other races. Neutral: influence (ext), colony bonus, productivity (int), goal: minimize interactions with others while focusing on own development/research, passively influence other planets into submission. Evil: conquest, military power (ext), military production and support (int), goal: conquer all others directly. The special abilities and projects of the alignments should reflect their objectives; just my opinion. I am trying to provide more substance for the alignments. Special buildings outlined below should require certain research paths or their own tech in an appropriate location in the tech tree; a civ wide building could also be replaced with an alignment-specific tech in some cases.

Bonus Suggestions that fit Goals, make all choices viable, and add variety:

Good: 50% colony maintenance (civ wide). Diplomatic bonus (+50% or appropriate). Reduced ship maintenance (-25%). A new building (1 per planet) that prevents invasion tactics that harm the PQ of planets (or eliminates the PQ damage of those tactics, maybe protects against spore ships too) "Planet Protection Center". Standard defensive techs/bonuses. A new building (civ wide) that increases the minimum defensive rolls of ships in orbit of a planet by +25% (like luck, but only for defense rolls) "Galactic Defense Network". A new building (1 per planet) that increases the final invasion advantage of the defending planet by +50% "Mobile Medical Facilities". A new building (civ wide) that increases the diplomatic penalties for a race declaring way on you (or hurts their relations with other races) "Hall of Sympathy". New modules for military starbases that increase ship defense by +10% each "Defensive Grid I/II/III" (max of +30% from this effect).

Neutral: Instant terraforming. +10% morale bonus. +10% Economy. +25% population growth. +50% loyalty. A new building which gives +50% influence (like 2 cultural exchange centers) "Cultural Think Tank". +10% influence. +10% trade. A new building (civ wide) which gives a small chance for minor races under your sphere of influence to flip to your side each turn (even if not at 4x influence) "First Contact Protocol". -25% cost of buying ships and buildings directly (both the immediate cost and lease payments), intended to replace the "+25 interest" bonus which simply reduces length of leases (but doesn't help when using the pay-in-full purchase option). A new building (civ wide) which increases the chance of a planet flipping (when applicable) based on its morale (lower = higher bonus, slightly exponential so minimal effect above 50% morale, large effect when very low morale) "Neutrality is Happiness Radio Network". +5% bonus to all economy starbases (automatic). +25% bonus to all influence starbases (automatic). A new building (civ wide) that increases research by +10% "Universal Research Algorithm" (perhaps from a neutral tech requiring Neutrality Learning Centers). A new building (civ wide) that allows a cultural warfare invasion tactic (similar to information warfare) where a percentage of the population joins the attacker based on the cultural influence ratio of the attacker to the defender for that planet (higher influence = higher percentage of the population joins) "Neutrality Propaganda Center".

Evil: Standard evil weapons techs. +10% military production. +10% ship attack. +10% soldiering. No starbase maintenance or upgrade costs. New modules for military starbases that increase ship attack by +10% each "Weapon Amplifier I/II/III" (max of +30% from this effect). Mind Control Center effects changed so that planets near cultural revolt roll twice to see if they flip to the owner; also gives +25% population growth civ wide. A new building (civ wide) that allows a telepathic invasion tactic that gives no combat bonuses but if the attacker loses then the defending planet has a chance of subverting to the attacker anyway (25% / SQRT(planet_population_in_billions)). A new ship component for creating kamakaze ships, "Quantum Bomb"; A ship with this component self-destructs rather than attacking, rolling with an attack strength of the ship's maximum HP, hitting a random enemy ship, and ignoring defenses; tie rules still apply, so this ship cannot win a battle on its own. A new building (1 per planet) which adds +25% MP production (like a power plant) but also a static -25% morale penalty (after all other morale calculations), "Slave Labor Camp". A new building (civ wide) which allows spys to poison 50% of a planet's population, but destroys the spy in the process, "Cruel Spy Tactics".