Take every "exploit" that was made possible by logic or complex designs that was ever removed and put them back in, then add some more. Then approach the whole thing from the perspective of balancing their difficulty to implement with a reasonable ROI instead. The BEST part of this game has always been that technology comes from actual RnD and not some timer fed by tech points or sliders in a chamber system. Starmades isn't about grinding to make a better ship, you innovate.
Personally I feel some of the best patches in this game were the "hack-job" patches. Like when chain drives were limited to 30ish hz pulses so that you still had reason to make complex logic drives, but could not build super unfair X-drives and before it was dumbed down to just need a simple not-delay clock, or worse... chambers... At some point there were no less than 5 very different approaches to the chain drive problem, each with their own strengths and weaknesses, but all better than the out of the box approach. It gave factions unique design philosophes. Being Thrynn or Vaygr or MagicTech was not just a name, it was the collective secretes your faction had discovered.