Its a great idea..
There are 2 things in this game that I dont like so much.. you get some bonus without a good reason.
1st is the space anomalies.. just put some spots on the map and send survey ships to explore them and you get a random bonus..
2nd the bonus resources.. military, morale, research and economic. Built starbases and you increase them..
What Jae suggests is a much better idea instead space anomalies.
Lets say we forget the idea space anomalies and instead we have some real ones but very rare that can appear anytime even like a mega event, like black holes, supernovas and other space exotic stuff.
And most common for survey ships or ships equiped with a lab they can scan solar systems, the sun, the planets their orbits. And depended on their sensor technology they can find more or less.
Using just the sensors of the ship or even send an away team to investigate a planet. Sometimes we will be unable to investigate before we advance on sensor technologies or we research a special technology. And here we could have a mega event like a virus that spreads all over the galaxy or an artifact that advances our civilization.
On the 2nd the bonus resources would be much better to scrap them. Yes they help they are good.. but.. morale, military points? You extract something and people get happier and soldiers better? Its no sense..
I say then again when the survey ships scan the planets they can find ancient scripts or devices that can help to find ways to improve our morale and military. Additionaly on some planets colonizable or not we can built bases to extract minerals that they help the economy or bases to study something on the planet that gives us a research bonus. (when the study is over the base closes)
Sorry for the exteded text..