at this point the engines, shield, deflector, and consoles are the same as the Atrox with the difference being the atrox shield hp is around 14k and the nebula shield hp is at 16k.
i'm still testing what shields are better. so far the MACO seem better overall then the aegis.
Tbh, you're missing the whole fun part about the Nebula, having flown one myself for quite some time. If you are hitting 16k shielding, there is no reason for you to have two armor pieces in engineering console slots--one will definitely suffice. With skills, your hull should be a good amount over 40k, which, when combined with skills, makes you pretty much unkillable in PvE. Also, it looks as if you're using dual beam banks for the Atrox, but not the Nebula?
Then again, it's hard to tell how successful other people will be with these ship builds if you don't like your own skills, or what powers you have assigned to your Boff stations. My Nebula has ~13k shields, and it tanks just fine with its large amount of debuffs via powers and consoles...and I only use one field generator, not three. I can only comment on the Nebula build, anyway, as I have never flown a carrier, so that looks fine to me.
But just note that the Nebula has a fairly high turn rate, considering its a hybrid cruiser/scivessel, so beam arrays are somewhat wasted.