Are you referring to Bridge Officer abilities, traits, skills, or something else (or all of the above)?
How do you want to play your character? Do you want to fly an escort with a bit more survivability and a bit less damage than a tactical officer? Do you want to fly a nigh-indestructible cruiser? Are you going to focus more on PvP or PvE?
In general, as an Engineer you'll want to leverage your survival and energy management powers more than anything else, but there's a lot of ways to play.
Mainly referencing Player Skills but Boffs as well. Beam boats are fun for me becuase they are good at survival but can do decent damage with beam overload. I want to tank Mostly pve on the fed side,(already have a va tac)
Most cruiser pilots prefer to chain 2 copies Emergency Power to Shields to maintain high levels of shield resistance and shield power (which gives more shield resistance). Complimentary Tactical ability would be Tactical Team (for automated shield distribution). Complementary science abilities would include Transfer Shield Strength and Science Team (and Hazard Emitters and perhaps Polarize Hull when facing the Borg).
If you want to run a hull tank build rather than a shield tank, you'll want a copy or 2 of Auxiliary Power to Structural Integrity Field, maybe Emergency Power to Auxiliary to boost those abilities. Complimentary Tactical ability would perhaps be Attack Pattern Delta for some extra hull damage resistance. A complementary Science ability would definitely be Hazard Emitters.
You'll want at least 1 copy of Engineering team in any build for restoring disabled systems and some hull healing, perhaps Science Team to purge Subnucleonic Beam in the few instances where it shows up (Hirogen and Breen), and perhaps Tactical Team for purging Borg Boarding Parties (and in the shield build, as noted).
If you tend to want use Arrays and Beam Overload, you'll also probably want a copy or 2 of Emergency Power to Weapons to overcome the extra weapon drain.