I have been noticing that the chosen systems used during Auto upgrades are not even remotely smart choices. They are instead chosen purely on their position on the tech trees. Higher on the list, or Further to the right and that is the system used. Regardless if it is in any way better or worse.
For example, I had the first tier HyperFusion reactor tech, and after Retiring some found ships I gained the Advanced Fusion Tech. Because the Fusion tech was one column to the right the updater wanted to replace all my reactors with Fusion, which only produced 2/3 the power of the one column left HyperFusion, and would have left my ships and bases Energy starved.
Same thing with Reaction engines, Quantum is always chosen over Acceleros. Shields, Hyperdrives, etc... are all handled the same way, weaker shields chosen because the they are towards the top of the screen, slower Drive, weaker Weapons...
Maybe a behind the scene score, a player selected preference check box, or a smarter AI could all be of benefit.
Until then I will be doing manual updates, but that gets repetitive and very old fast.