kine First ship, anything that takes out a flak also tends to take out an ammo factory, causing them to explode. This takes out the nearby shields and damages the walkways. Engine rooms are far away, consider bringing them closer by swapping reverse thrust and lateral thrust or use conveyors. Farthest shields have poor regeneration. Dedicated crew or power storages, as Jarvis stated, will alleviate this.
The flaks can't focus fire at close range due to narrow firing arc.
It can shut down projectile based ships, but it's in trouble against anything else.
Second ship, ion combination is inefficient. Front is heavily armored, but everything is just so far apart. Shields are far away, ions are far away, engine rooms are far away. Shield regen takes a hit when so far from the reactor. If you're going to use a large reactor design, crew assignments become more important, especially dedicated power storage crew. CRs are exposed.
Pick either ship to fight either ship.
I_Am_Jarvis Running off a single medium reactor doesn't necessary mean it needs storages. Storages are only really useful for mitigating crew delay over distances or for allowing brief bursts of energy use.
