You only need to scan about 10-20% of the planets, no-where near enough upgrades to use it all.
I scanned all but three systems to Poor/Depleted & ended up with ~1.5mil of spare resources.
Just look for an Element Zero guide and scan those planets, you'll get the rest of the resources needed on the way.
How come I have scanned almost the whole galaxy now (about 70% at least) and still I have not got enough of Platinum for all my upgrades?
EDIT: Maybe I am doing something wrong, I only get like 2-3k per resource when I scan.