This is a general Guide to improving your STF performance. It is geared towards beginners who have no idea where to start with how to equip their starship. I made this for my fleet and thought I should share it here. It is not meant to be the definitive guide but a starting point.
Before you start running STFs you should run the missions "Assimilation" and "Past Imperfect" for the Assimilated Module and the Paratrinic Shield Array.
The number one thing to know is that STFs are on timers. This means that DPS is king at completing optional objectives. Most importantly, use one type of energy weapon. I recommend Phasers for Starfleet and Disruptors for Klingons. Personally, I don't use Torpedoes or Mines at all. I would recommend not using them but it's not a huge deal if you choose to. If you do, please limit them to one.
Choosing a Ship:
It really doesn't matter what type of ship you choose. In my experience the most important thing for STFs is DPS and that is directly tied to how many tactical console slots you have. So generally speaking ships with more tactical console slots are better than those with less. That being said, use the ship you like the most.
Fill your tactical slots with Phaser Relays or Disruptor Induction Coils respective to your weapon type. Your Engineering slots should be all Neutronium Alloy. Your Science Consoles should be Field Generators and Shield Emitter Amplifiers. Cram the Assimilated Module wherever you have room, but NOT in a tactical slot.
Shield; Engine; Deflector:
Borg. They can be redeemed for 5 EDC a piece at Roxy in Deep Space 9. It is listed under the Retro tab. Use these until you earn the MACO Shield MK XII. Then use the three other pieces of the Borg set and the MACO Shield. I recommend running Normal STFs until you've earned the whole Borg set. After that you should be able to handle Elite STFs.
Bridge Officer Skills:
These setups will work with pretty much any ship in the game.
Primary: Tactical Team 1 / Cannon: Rapid Fire 1 / Attack Pattern Beta 2 / Attack Pattern Omega 3
Secondary: Tactical Team 1 / Cannon: Scatter Volley 1 / Cannon: Rapid Fire 2
Primary: Tactical Team 1 / Beam: Fire at Will 2 / Attack Pattern Beta 2 / Attack Pattern Omega 3
Secondary: Tactical Team 1 / Beam: Fire at Will 2 / Beam Overload 3
Primary: Emergency Power to Shields 1 / Engineering Team 2 / Extend Shields 2 / Eject Warp Plasma 3
Secondary: Emergency Power to Shields 1 / Reverse Shield Polarity 1 / Aux to Structural 2
Primary: Hazard Emitters 1 / Transfer Shield Strength 2 / Tyken?s Rift 2 / Gravity Well 3
Secondary: Polarize Hull 1 / Science Team 2 / Tractor Beam 3
Skills not* to use:
Dispersal Patterns; Emergency Power to Auxiliary; Auxiliary to Battery*; Auxiliary to Dampeners*; Boarding Party*; Aceton Beam*; Jam Sensors*; Mask Energy Signature*; Tachyon Beam; Charged Particle Burst; Feedback Pulse; Photonic Officer; Scramble Sensors*; Viral Matrix*
Most important skills and how to use them:
The following skills should be on every ship that can outfit them. Use Attack pattern Omega, and Polarize Hull for tractor beam breaks. Use Tactical Team to keep Shield facings up. Emergency Power to Shields should be up at all times for the resist boost, so you need 2 copies. Attack Pattern Beta is a massive DPS increase. Aux2SIF and Hazard Emitters are for Hull healing. Transfer Shield Strength and Science Team are great for healing others. Gravity Well is the Ultimate Crowd Control, and Tyken's is great for crippling enemy attack damage. Before you use any Science skill change your energy settings to something that has at least 50% Aux. Then wait for it to reach its max. If this means waiting a few extra seconds before shooting off a Gravity Well so be it. Afterwards, switch back to Attack settings. It is better to have a slightly late Science skill than one that is ineffective.
Lastly, damage is determined by distance. The closer you are the more damage you do. You also receive more damage the closer you are.
Thank you for your time. I hope you find this useful. If you have any questions please ask.
I personally would say running 3 or 4 piece borg is right, but do it only until you can get the MACO XII shield and deflector as well: it's better for the majority of builds.
Always use the MACO shield if possible, but the deflector has generally better stats than the borg deflector, and the 2-piece bonus is totally under-rated. The bonus from 3 piece borg just doesn't seem to happen enough for me to be worth the worse stats, and a passive 5% global cooldown reduction is a better way to go, I think.