I've been experimenting in the simulator a bit and I think there are two big problems I see:
1) Doom has serious issue with unphasing near its own mines. It does this regularly against sim paragon with an aggressive officer, even with the elite phase skill that makes it very fast (did it in 2/3 tests, happened to kill the paragon somewhat quickly in the other test). I'm actually suspicious that this is the cause of my doom taking lots of damage in battle, not the enemy.
2) There seem to be issues where if the enemy is high on flux, the doom never backs off, even if it is also high on flux. I think this is maybe just aggressive officer behavior and not doom specific, but it can be quite suicidal. I don't mind staying to try and finish something off, but there are lots of ships that are not actually vulnerable because they are high on flux (due to high armor and good PD), and staying to fight on high flux is suicidal for the doom against those ships. Maybe aggressive AI on phase ships is just bad? I'm not sure. I would like if it backed off to vent when both ships are high on flux. A lot of time the enemy does not have time to vent in that case and you can easily kill them with a fresh flux pool.
edit:
3) Doom 'relaxing' after securing a kill (un-phasing, venting etc) even though there are still threats like a final volley of projectiles, or mines or missiles and take unnecessary damage.