good thing I searched before posting my new original suggestion...
I would like to see some kind of implementation of the reactor room with a console operator.
After scanning this thread, the best ideas I think to balance in my view would be like this:
1 hitpoint = 1 power bar
Room should have very tough armour because a reactor is a very powerful thing that needs extremely strong containment, so say 50% chance of negating all damage, 30% half damage rounded down, 20% full damage
and/or
Room can only be damaged by beam/hull weapons that can cut deep into the hull. Room can be targeted by all weapons, but non beam/hull weapons cause damage only to hull and crew not reactor. Neither would fire damage the reactor, safe in its fusion proof containment.
a combination of these 2 ideas would make targeting the reactor a difficult choice, requiring many more shots to cause serious power deficiencies. Much quicker to take down shields or weapons by targeting appropriate systems.
Another idea could be for each bar of damage the reactor takes a cumulative percentage chance of reactor overload causing either 20% detonation instant kill or 80% complete shutdown requiring restart sequence after taking a cooling off period, 1% for each bar damage or less (0.5%?), cooling off for restart takes total output in seconds, after which reactor is restored to previous power output including already sustained damage.
Repairs would work as normal.
An operator could grant some timed abilities, like overcharging a system allowing for more weapons or shields power or simply more total output for a brief period, increasing in length with engineers skill rank - 10s, 15s, 20s. Overcharging could carry some risks of overload but result only in shutdown not detonation due to system fail safe. smaller chance of overload for more skilled operator. - 10%, 5%, 2% This would allow early game ships to briefly take advantage of having a larger power output, keep shields and drones and weapons up simultaneously albeit for a short time, balanced against the risk of shutdown/restart.
Wow.

As soon as you get thinking about an idea for this game it starts cascading. I respect that the developers have kept simplicity above more complex systems, and that that principle is largely responsible for the smooth and fluid action and (to my mind) impressive balance for a RNG game. It's just that the depth is a little bit limited, take the original rogue for example, I've been playing that for decades and every so often I still come across a monster or item, be it a ring or staff or scroll or potion etc. that I have never seen before.
To be honest I'll not worry if nothing changes, I haven't found a single bug in 80ish hours of playing and I still haven't beaten the final boss yet! nearly did with the Zoltan A but I had to repair after phase 2 which left me 1 beacon behind him as he charged towards the rebel base. That was so frustrating.
Regards,
Sam.