I see, for me I unlocked all the upgrade first (though not fully upgrade all of them, just buy the 1st upgrades) so I could see what upgrade options I have. Then I upgraded what seems to be the most useful, which include all of the missile & grenade upgrades, the poison shrinker's damage, the shrinker's cost, the attractor tool's cooldown, area, & strength, as well as the orb regeneration & payout multiplier upgrades. I don't know how other plays, but had the knowledge points be more generous, I likely would've upgraded everything first before going to the next level, but once I notice the slow down, I began saving points (though even then it's still extremely slow).
I hope my pov was a useful reference. I really want to complete the game but I don't want to wait that long for points to gather. Maybe introduce an upgrade that makes gathering knowledge points easier, I would definitely dive head first into buying that since (in most cases) it's a good long term investment that would help buy the other upgrades.