I think I would really prefer that energy upgrades are equivilent to ore upgrades in both the number and effect of upgrades, and obviously the energy distribution rate should be equal to demand if the energy is availabe.
The problem now appears to be that because highscores are already submitted, and noone is willing to wipe them to allow a fix to what really seems to be a defect in the game, so regardless of any solutions anyone comes up with, There is no possibility of a fix.
Reading your first and last posts, I do not see what the issue is that you claim is "broken" and needs a fix.
In ancient pre-beta history, Karsten75 was probably responsible for some of this issue. The early versions of the game would use ore and gem resources before depleting any resources generated by reactors or rigs. He complained that this seemed illogical to tap a source that need not be depleted while the energy production from reactors would go to waste if there was no storage for them. That seemed to make sense and Virgil switched the algorithm to consume first from the generated resources and then from the resources that could be dug up. I hope this much is clear to all.
Then later, in beta, it became apparent that for those with huge farms of resource generators, it would never be possible to utilize the gem energy, since all energy needs for "normal" consumption could be met from the generated resources. At this time Virgil introduced a clever little gimmick in the game. One could, if one had an inventory of resources, consume those resources at the rate of the stored resource (energy in this instance).
This brings an interesting wrinkle to game play. If one is careful in husbanding ones mined resources, the energy cap becomes less of a limitation and makes certain strategies possible - the best demonstration I've seen of this was Kithros's famous video showing how he did Day 20 in the story missions without using one single unit of stored energy - giving him the theoretical ability to use 2,000 energy/sec in a final assault.
If you see this as a defect that affects game play, I'd like to read a justification for what aspect of the game it breaks and why it should be changed.