Has it been considered to add more surprises (and FUN) to the colonization efforts by adding anomalies and oddities? Basically a system body can have from 0 to 3 oddities that might be good or bad. Some will require efforts to deal with, some are permanent or passive.
Nothing super original compared to others games, but this is akin to the concept of 'Goody Huts' for Sid Meier Civilization. Really, I think all Sci-fi 4X games have this kind of stuff on their planets (Endless Space, Stellaris, Galactic Civ III).
This can require a bit of efforts in writing so they are diverse enough, but I'm sure a lot of us would gladly help.
Can also be seen as an extension of the current ruins feature but more diverse. It can be about a dangerous semi-intelligent animal in a jungle world, some left over nanite cloud in a chasm of an asteroid, a strange (abandoned?) pyramid in a desert world, etc. The more the merrier. It would add mystery and thrill and make system body more unique also.
There is no need to create a complex 'event system' to deal with these oddities. Either you leave it alone and it add a passive effect or you click on the 'handle the issue' button and it solves the issue. In both cases, you spend (or earn if a good event) resources (colonists, money, supply etc.).
"Ah yes, this planet. A nice one now with 10 millions colonists and 100 industries, and good corbinite concentration. But these seemingly intelligent octopus in the sea are posing problems as they tend to mind-control unwary colonists."
Passive effect (per month): Loses 0.1% of colonists total
Solving1 (button A): A massive effort (cost 50.000 money) can be undertaken to get rid of these octopuses in the sea by adding a targeted neurotoxin in the water.
Solving2 (button B): We can put these octopuses (pi?) in a natural reserve and study them (cost 250.000 money). This will prevent any nefarious activity while giving us a chance to study them (1% a month to gain 500 RP in Biology)
Etc