You can install things individually too, but typically youll just want to use binary installs instead of source based installs. A full binary install will get you the latest changes for everything though.
The only way you can remove systems right now is manually from the /opt folder. I agree that its waste of space but most of the users of retropie like the idea of a premade system thats just ready to go with everything they need.
We’re looking into making a more modular menu that will make it easier to remove the things you don’t want.