The organelle upgrade costs should be determined with that in mind. Also the way upgrades are, in my mind, meant to be really different ways the organelles work. It wouldn’t be so bad as you wouldn’t want to blindly upgrade all of your organelles with the same upgrade. That’s a really huge reason why the original organelle upgrade plans specifically called out to ban just flat out “upgrades” to make an organelle more efficient. Instead they should fundamentally change the organelle to add different gameplay options.