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Either halve or remove pop penalty on technology.
Likely increase core worlds or restore direct democracy to +4.
My preferences are similar to yours in this regard, but I'm definitely going to play before messing with that kind of thing.
More trait points to pay with (what's the point of being super adaptable if I have to a bunch of sedentary weaklings who reproduce only once a blue moon?)
You can get more trait points during play with genetic engineering.
 
I'm looking to see what I can change from the 00_defines
 
Rare earth hypothesis. I'm going to significantly drop rate of habitable worlds and play in a gigantic galaxy. Other than that, figure out way to make desolate galaxies colonizable via dome / ring / superstructure of some sort. I've got a few ideas that I'm hoping to implement.