I was thinking of more 'passive' bonuses. Like automaticly producing a set number of resources even though facilities don't exist. Or tribes of natives that 'worship' the players race as gods (think Ewoks) that give bonuses to ground combat. Things beyond just upping/minusing the base planetary values. These can be added with the 'ability 1'/'ability 2' in the Map Editor but don't work. I had a full map of 'special' planets and sectors that should have provided bonuses like the ones described above and many more. But when I actually colonized these planets no values were added at all. Example, the planet I had producing 500 minerals/turn due to native miners produced 0, even after I added mineral facilities there was no added bonus.
I would just like to be able to personalize planets even more. The only ability I got to work right was the 'Random Movement' for sectors, I had a sector modded so all ships moved 3 spaces randomly/turn. Made for some fun

. These could be well used as there are even spots for planets to have 'storage space'. I added planets that should have been able to store 30,000 units of minerals due to 'cavern systems' but didn't work as well. Just think this could mimic the 'Starting Facilities' that everyone wants for AI startup to help with resource storage.
Hopefully this clarified what I meant.
------------------
"The Empress took your name away," said Chance.
Owen smiled coldly. "It wasn't hers to take. I'm a Deathstalker until I die. And we never forget a slight or an enemy." -Owen Deathstalker.