About Doom, in vanilla mines can exploit omni shields, but its only one phase ship which can exploit omni shelds, not fire through them, since AI can rotate their shields as they want. About mines, from one side what Omni AI gives high priority to mines is a exploit, which allows to create opening to fire reapers, from one side, mines also deal big damage so ignoring them is not good idea either, about nerfs, I think is good idea make Omni shields cover from them only if they about to explode, because they take some time to charge up, another idea, make mines as weapon, which can work in phase space too, so they are deployed at doom location, although i'm not sure if they will be useful this way. Also alot of subsystems seems like have bigger cooldowns in AO, I think mines with simply slower recharge time or less of mines quantity will be more balanced.
In 095 Doom very buffed because of skills some subsystems such as mines really benefit from subsystem skill.
And I think Phase Ships also actually need to be punching above their class, since they doesn't have shields, and can't avoid damage when attacking.
Also I just not sure if speed increasing abilities is useful on phase ships at all, they still can catch up enemy in phase because of time dilation, and i'm not sure is Plasma Burn and Maneuvering Jets are working in phase.