It's a bit weird - like often there will be 2 stars and it will say 51% complete. Had a look at whether it was related to '% system mass', but it's nothing that obvious![]()
I always assumed the percentage was based on a heap of stuff, such as the mass, the type of body, whether it has surface POIs etc...
Basically, scan a bunch of barren, rocky worlds and it won't increase the percentage much.
Scan a couple of ELWs and moons that have surface POIs and it'll cause a big increase.
It's not really something I've bothered to investigate too deeply.
If I'm bothering to scan a system at all, I'll just keep at it until it's done.
