I would like to suggest another, based on the planets themselves. These would come in 3 varieties, ones which the planets are 'born with', others that can be added by NPC/mission drops and some that are either. Most of these passive abilities could only be gotten once. They could stack (Space Station, Ringed and Exotic Spring) but you couldn't have 2 of the same (ex, 2 Exotic Springs).

Born:
Friendly natives (Terra): Working with the native population, you planet can sustain more life. All population building gain a 5% boost. Additionally, you get +50 population and +25 vs invasion. When planet becomes a Gaia, these bonuses double.

Unfriendly natives (Terra): These natives feel you are taking over their planet. They make it harder for you to do anything on the planet, killing any who wander off. -50 population however they don't want other colonizers either so still +25 vs invasion. A defensive building on the planet will cause their -50 to be ignored. When planet is turned to a Gaia, they change from Unfriendly Natives to just Natives. Natives realizing you are not there to exterminate them, stop harassing your people. Population negative is removed, invasion bonus stays.

XTS-9 production (Toxic): This planet naturally produces XTS-9: +2 Mining, +25 vs invasion, -5% population, +1 XTS per day.

Self-Cryo (Icy): Your planet is so cold that you can dedicate space otherwise dedicated to refrigeration units to MORE research: +1 research per building. (Melting the planet would lose this bonus. This might make having multiple smaller buildings actually better than more efficient buildings up to a certain point, I've not done the math). Becomes Hydro-Powered when melted: +1 research (not per building).

Ring (Any): +1 to mining or research or artifacts

Extinct Colony (Any): An advanced civilization was stranded on this planet and is now all dead: +1 Artifacts (not available on Terra planets with any kind of native).

Hydro-Farming (Natural Oceanic): Your sea is bountiful: +5% population, +2 Research

Natural Fortifications (Barren): The dirt of your planet is very hard when made into cement. This allows for great fortification. +150 vs invasion, +100 defense. (Stays when converted to Sentient Planet)

NPC/Mission
Gemcano (Volcanic): By seeding the core of your planet, you are able to get the volcanoes on the world to spew unnaturally large and precious gem stones: +2 mining, -50 cloak.

Ultra-Pure (Metallic): A process is added to your planet which makes the ore refined from it ultra pure however, it is so sought after you will lose planetary size rank: +5 mining, -2 building spots

Gas-Converter (Gas Giant): Permanently changes the research of a gas giant to mineral production, leaving very sparse research. (Could be destroyed by owner. So a Research Ex Rich would become a Mining Ex Rich with very sparse research)

Space Station (Any): +5 spots added to planet, can not be used for mining/research/artifact (or artifact type) buildings, essentially a weapons/defense/cloaking platform.

Ring Optimizer (Ringed): Changes the randomly generated ring on your planet to a type of ring of your choosing.

Corrosive Substance Launcher (Toxic): +25 attack and +25 defense to a planet, max 175.

Either:
Exotic Spring (Exotic): Your planet just coughs up exotic matter that is easy for you to harness: +1 mining & 1% more exotic material on mineral collection.

Hyper-Silicon (Desert): A special type of silicon is found on your planet that the Sha'din need for their Supercomputers. They are willing to trade special research knowledge for quantities of this: +1 Research (Upon crystallization, you get Natural Hyper-Crystal, see below). NPC could drop artifact allowing you to find Hyper-Silicon if not there when planet is colonized.

Natural or Man-Made Hyper-Crystal (Crystal): A special type of crystal is found on your planet that the Sha'din need for their AI Cores. They are willing to trade special research knowledge for quantities of this: +2 Research (Natural), +1 Research (Man-Made). There is a chance (10%?) that you will get Man-Made from changing a desert planet without the hyper-silicon bonus. NPC could drop artifact to allow Man-Made Hyper-Crystal.

Moon (Any): Your planet has a moon: +15 spots added to planet, can not be used for mining/research/artifact (or artifact type) buildings, essentially a weapons/defense/cloaking platform.

I like the idea of this ... can you give me some examples of the bonuses

Examples include veins of rare resources which boost mining output, or military prisons that reduce max population but increase defence.