Well, there are a few issues with that, but I get your sentiment - I myself actually like the gradual increase in power for my favourite ships as well.
However, I do feel you need to be a bit more critical of the system than that.
1) Engineers are mandatory to not die in interdictions when your combat rank is elite is based, etc., so for your ship to effectively be flyable in most situations you’d need a fairly highly engineered ship nowadays.
2) I doubt people wanted to max every build for every ship. For instance, my main ‘do anything’ ship, the anconda, would simply need a few spare modules for trading, exploration, etc., most of which I would only ever engineer once or twice. However, under the new system, I’d need to engineer them at least 3 times to get an acceptable-ish result, probably closer to 9-12. That is a major step down in that regard.
I have very few modules on my ships and have no issues getting away or killing elite NPC's. As to players, I am not that good so I generally run.