Alright! Because I'm getting bored of nuking things in a VA ship, I decided to harken back to something based on my favorite aesthetic design in Star Trek; The Exeter-class Constitution refit. I figured running VA missions in this would present a proper challenge.

Here's what I need help with: I have no experience at cruisers, be they low tier or high. What is the most viable BO power setup for the ship, assuming I want to maximize my best chances for survival/victory in higher tier missions, with the limited BO slots available?

Ensign Tactical
Lieutenant Engineering
Lieutenant Engineering
Ensign Science

I'd value any suggestions or input! I will update this post with my own ideas after I finish testing a few things out.

I'd stick with heals and buffs to try and keep yourself alive and protect against attacks. DON'T focus on damage, you won't be very good at it with the less weapon slots and lower BO layout.

Let others engage first if at all possible and help buff them or yourself while attacking intermediately, with an opportune torpedo or beam salvo. Stay in the back of a firefight and run if need be, coming back when you are healed and ready.

Throw in some disorientation and hamper tactics, like scramble sensors and eject warp plasma in order to stay on top of the fight.

That was off the top of my head.
-Quiiliitiila

Sage advice. Thanks muchly! Anyone else have anything to add on BO power ideas?

Second part is weapon layout; It gets two fore slots and two aft. I am currently running beam in both fore, and beam/torp in aft. What would be most ideal for the abovementioned disorient and hamper tactics?

Sorry for the late reply, I went out for dinner...

Anyway, here are some useful BO abilities for your ship:
ENGINEERING:
-Boarding Party
-Eject Warp Plasm
-Engineering Team
-Aceton Field (Possibly, I can't vouch for it's usefulness. In theory it would be good for keeping their weapon damage down)
-Emergency Power to Shields (run this for as long as you can, it'll help mitigate the damage you take)
-Emergency Power to Engines (RUN AWAY!)

SCIENCE:
-Science Team
-Hazard Emitters
-Polarize Hull
-Scramble Sensors

TACTICAL
-Attack Pattern Delta
-Dispersal Pattern Alpha or Beta (whichever you prefer)
-Torpedo: High Yield

Whichever of these you choose depends on your play style entirely, I figured with any of these you could do hit and run/hamper tactics and keep the enemies from doing tons of damage or moving around. I would HIGHLY suggest teaming with someone who can take the brunt of the damage.

For weapons, I suggest 2 Tetryon beams (their secondary drains shields). One fore and one aft.
and some type of mine in the aft (I'd suggest Quantum for damage and crew Xing). Perhaps a Quantum or a Tricobalt in the front.

If you are teaming, focus on using your abilities to their best effect and opportunely sinking in a Tricobalt or Quantum when a shield facing goes down. Otherwise focus your attacks on one shield facing if possible until your torpedo can be used to good effect.

Hope that helps! Let me know if anything works, or what you find.
-Quiiliitiila

I really appreciate all the advice and help with this, Quii! Thanks a bunch. Here's the setup for BO powers I'm thinking I'll run at present;

Ensign Tac: Torp High Yield
Lieutenant Eng: Emergency Power Engines, RSP
Lieutenant Eng: Emergency Power Shields, Engineering Team II
Ensign Sci: Polarize Hull

Hey, no problem :^D

Anyway, you may want to choose something different than RSP because... Well because I've used it and in my honest opinion, it is not worth the BO slot. The six seconds of immunity and shield heals, does not make up for the RIDICULOUSLY long cool down.

Perhaps Aceton Field or Eject Warp Plasma?

-Quiiliitiila

Ah, right. Forgot that RSP got nerfed a good while back. XD Shows how long it's been since I ran a survival build, huh? I'll go with Warp Plasma instead, should be quite handy.

And actually, after testing a bit, this is the weapons layout that seems to be doing the trick for me-
Fore: Retrofit Phaser Beam Array, Quantum Torp
Aft: Retrofit Phaser Beam Array, Breen Transphasic Cluster

I was surprised at just how much punch the Breen Cluster mine/torp can pack in PvE. And since with a heightened engine power I can turn quickly, broadsiding with the two Phasers has been getting shields down fast. Plus the blue thin-beam Phaser graphic is aesthetically pleasing.

I did a similar thing for my Exeter but this is what I had for BOFF skills

Tac - High Yield
Sci - Sci Team
Eng - Emergency power shields, emergency power weapons
Eng - Reverse shield polarity, Engineering team II

Not very hard hitting for DPS but it can last better than you'd think at VA level.

Yeah. I am pleasantly surprised at how GOOD the Exeter can perform in VA missions. I just completed all my PvE dailes with mine, and had no trouble(though admittedly the fights were longer, but what do you expect from a ship with only 4 weapon slots?).

I'll update the OP with my working setup for Exeter shortly.