Maby its just my play style but its always bugged me that i can just shift upgrades around to different machines that i am using.
My suggested change is to make upgrades permanent, In a way similar to Thaumcraft, You may ask "But what if i want to move my machine?" lets call machines without upgrades stock machines and machines with upgrades modded machines.
If you wanted to move a stock machine it would behave in the same way that they currently do, dropping a block that can be stacked. on the other hand, if you were to move a modded machine then it would drop a unstackabkle block that still maintains the upgrades.
(Going to add them in afew minutes)