The devs did actually add a method of balancing engineer power. The game throttles the difficulty based several factors, the 3 biggest are:
1) bounty status
2) ship DPS /type (these are 2 independant variables)
3) presence of engineer mat cargo
So they effectively make it a gauntlet to get the mods in the first place, and then they make it so that if you misuse your powers, you will face an army of extremely deadly assassins. Now of course you can go back to playing a mid tier, unmodded ship, devoid of engineering cargo, and the difficulty spikes will virtually disappear. I guess you can argue about the realism of such a throttle mechanism, I personally think it makes sense, but the effect on gameplay means that there is a comfort level of difficulty that anyone can dial in to their exact preference.
Enemy auto-scaling like this essentially means you grind the grind just so that nothing ever changes, because as soon as you get benefit X, enemies get benefit Y to compensate. For better self-balancing gameplay, a game should have geographical regions of different difficulties, so that the player can at all times choose where they go and thus what kind of opposition they may face. ED actually has the foundations for just that: security level. Enemies should never at all scale based on anything related to the player, only on 2 factors:
- What system you are in. A more sophisticated solution would also consider locations within a system, e.g. in orbits around a planet which has a pirate base = more pirate encounters.
- What missions you have active. Obviously if you have a cargo transport mission that is rated at "elite", any enemies that are spawned as part of the mission should be of corresponding difficulty.