Ran into a few problems with this game, namely the barrier and Core mechanic seemed pretty weak, and the chance of Attack Matrix causing a wipe from full strength if you roll bad sucking the fun out of that fight.
For reference we always play with no don't panics and the Ouroboros shuffled into the deck.
So our rule changes:
1. Each threat card can only activate once per threat phase. This only affects Attack Matrix and Cloaked threats, and causes them to increase your odds of activating threats, but no double whammies. (like double 6s wiping your ship from full strength)
2. Core activation (6) heals every threat 1, and further, it brings back any destroyed sections of the Ouroboros at 1 health.
This one is a lot of fun, because rolling a 6 gets you a second threat roll with all of the Ouroboros in play.
I posted this now because I've finally beaten the game with each ship using this variant.
I also don't let the Quantum Cannon put any Ouroboros pieces back in the deck, because that is cheap.