Well the title says it all really, currently VA with aegis shields and deflector, borg console and engines. But which of these engines is better for combat? I'm currently using my flagship (excelsior refit) and whilst we're here with the shields should i use shield emitter amplifier or the the other shield console.

Tacticals benefit from the Aegis engines, as its boosts a skill that increases many of their captain abilities (especially Attack Pattern Alpha). I do not have it (so I can't account from personal experience), but in system space, the Borg engine seems inferior to the Breen Engine (Breen has better stats). Though if you want Warp 14 or Borg set bonuses (the first 2 are a shield and hull heal, respectively, that have small chance of activating on any damage dealt to you), obviously go for the Borg engines.

The ability to go Warp 14 isnt important at all, in fact some of the other non-aegis impulse engines that you can research have better stats than both, but if you want the special benefits...

Go for the Aegis impulse engine.

I would suggest both if you don't mind switching engines when you enter and exit a system for the Warp 14 boost from Borg Engines or Aegis if you want to stick with one. Personally, I would use the Borg Engines, but only because my main captain is a liberated borg with 2 liberated borg boffs and most of my bridge officers have the 7 of 9 implants.

Don't discount the Breen engines. They're cool.

On a cruiser like the OP is flying..... Borg engine.
Better the full Borg set

Do not discount the full borg set on a Tac/Escort. In my tac/raptor the highest numbers I have gotten are 1.32 million damage and 1.05 million healing

Through my tests, I have to say the Borg set plus aegis deflector is the way to go. All one needs to make the Borg shields more sturdy is add a shield capacity consol. 35 percent more shield from the consol, all the Borg set perks less tractor beam, tends to make my def r more survivable.

Again, a lot depends on pilot style, consol use, BO powers, cpt type, and consumables.

Aegis for combat, Borg for flying through sector space. Simple.

Bingo, don't use borg engines exclusively for this, only for Borg set bonuses.

The final set bonus for all 4 peices is a tractor beam with a long CD so don't worry about it too much, but the 2 and 3 peice bonuses are very nice. Look at which deflector compliments your powers best, if Borg use that and the Aegis shield, other way round if Aegis deflectors benefit you more.