I want to be able to upgrade my commanders so they are using the latest parts. By upgrade, I don't mean promote to admiral. They suffer from the same problem I want fixed. The problem I have with commanders is they use a hyperdrive plus engine. This remains true regardless of what tech you research.
They don't ever get better engines. Ironically, while they boost the speed of your fleets with their abilities, they can also slow you down because they are stuck using inferior engines.