I am new back to the game, the last primary reputation set I have marks in is Task Force Omega is anything from that rep viable for a carrier like the Vanguard or should I start collected a different sets marks, I have 3095 omega marks so would prefer not to let it go to waste.
I have a polaron build (makes sense with the ship) with the borg 360 cutting, plus a 360 polaron rear, aegis set (only one I could find) and 3 polaron beams forward with a quantum torp.
I play mostly PVE and enjoy all of it.
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For weapons I run 3 dual beam banks (inhibiting polaron) forward, along with the morphogenic polaron torpedo. Running a polaron omni array (crafted, think you start with one as a jem) and morphogenic polaron energy weapon on the rear (it's a hybrid cannon/omni beam).
The morphogenic set is really good if you want to stick with polaron. You have to run one of the gamma episode missions a few times to get the full set - it's got a console, torpedo, and energy omni weapon, and provides some nice boosts to polaron damage. The torpedo also does polaron instead of kinetic damage, and gets boosted by your polaron energy tactical consoles, making it more effective than a kinetic torp in the same build.
Upgrading your gunboat pets to at least the VR version from the dilithium store is a pretty good first step. It's a lot of dilithium but maybe you've got some to spare with that many marks hanging out.
As far as rep... if you want to stay with polaron, start leveling either gamma task force or delta alliance reputations (or both). I went with gamma task force for now, almost T5 rep with it, and will work on delta later. Both offer additional types of polaron weapons and some nifty sets to go with them.
for my ability setup, I'm running 2 copies of beam fire at will, 2 copies of torpedo spread, and tactical team for my tac abilities, keeps good uptime but in the future i'm looking at changing that so i can drop to just a single lt commander tactical (probably go with fire at will x 2 and tac team x1, and use the entwined tactical matrices ship trait to get free torpedo spreads out of it).
I'm using gravity well, intelligence team, and the usual sci/engineer stuff (hazard emitters, transfer shield strength, emergency power to shields, etc.) for survivability.
Intelligence team is a really good ability to slot once you can use it - it basically acts like a cloak, stopping enemies from firing at you for a few seconds, but you can still fire your own weapons while its active. Once you get the t5 mastery unlock for the carrier, using any intel ability will also buff all of your pets' damage/defense/stealth levels.
The biggest tip I have is make liberal use of your wingmen's polaron strafing run. I always link my wingmen (there's a little link icon on their interface) so that using one of their abilities causes both to use it. If I hit a group of enemies with gravity well to pull them together, and then use their polaron strafing run + torp spread/fire at will, those enemies melt within a few seconds in most cases. The strafing run is a really powerful AoE attack and i've noticed that a lot of people using the jem vanguard ships end up ignoring/not using their wingmen abilities much, which is a huge mistake IMO. The shield draining ability they have is pretty crappy, I never use it except on things like the current featured TFO where they can drain the station shields really quick, but the shield/hull heal ability they use is pretty good too, and has saved me a ton of times when my heals were on cooldown. Get used to using their skills like they're your own.
If you're able to, I would highly suggest picking up one of the fed/kdf escort carriers (whichever faction your jemhadar is allied with), and level it for the t5 mastery trait as well. The trait on those applies beam: overload or cannon: rapid fire to your pets whenever you use it.
If you can afford it, the next thing to go for is the wing commander space trait on the exchange, it's a must have for carrier captains. It causes all of your hangar pets to level twice as fast in combat, which means you only need about 1-1.5 minutes in combat for your gunships to hit 5 star rank, which makes them far tougher and boosts their effectiveness substantially.
Omega reputation has become somewhat outdated (though you should still definitely get the assimilated module for the crit). The cutting beam/assimilated module 2set bonus isn't really worth it anymore - every now and then it offsets part of a firing cycle's worth of power drain, but you get more damage overall from just rolling with other sets and forgoing the cutting beam.
If you're Fed-aligned, telbasta's advice will probably work the best for you - however, if you're KDF-aligned, or flying the Vanguard on a Romulan, the Dynamic Power Redistributor Module's 2set bonus + the Nausicaan Entoiled Technology set + the House Martok 2set becomes a worthwhile alternative. Either way, you're definitely going to want BFAW3 and Torp Spread 2 (at least) and probably a respec to put points into projectile weapon damage, as energy torpedoes can deal a huge amount of AoE damage and are a major part of beam builds nowadays. Besides that, there are consoles like tachyokinetic converter, zero point energy conduit, or fleet neutroniums if you need some resistance+turnrate. Basically, whatever area your build is lacking in after key set bonuses/standard fare, take what'll improve it.
As for your set, you'll want to collect competitive marks - the competitive engines have a great maneuverability buff applied on use of tactical abilities and the shields have a 5% chance to grant you crit every time you get hit by energy weapons (which will be often if you're in threatening stance + dealing high dps) (threatening stance should be active with high dps because you're going to be public enemy #1 anyway, so you may as well get bonus hull from it). The 2set also buffs a few things like weapon specialization and control. You'll want the elite fleet [ColCrit] intervention deflector from the Dranuur colony, and whatever core you fancy (I use Kobali for the AoE shield-heal-to-full panic button, others like the competitive core or fleet spire ones work great too).
If you can afford it, Self-Modulating Fire is a great trait. Rep traits boil down to stacking crit, skills boil down to basically filling out the tac tree (the only ones I wouldn't take on a carrier being anything past the first level of defense), impulse speed to keep up, and basic survivability skills.
You definitely want Override Subsystem Safeties 3 (which means from your skills, you'll want that early-on science tree control resistance buff to almost totally negate the offline debuff from this) and Grav Well 3, alongside standard-fare eng team/sci team/tac team/weapon buffs. Beyond this, it's largely up to you. You can bother with aux2bat for more cooldown reduction, stick to photonic officer, opt for more survivability, or fill all of your non-standard-fare slots with eject warp plasma and transfer shield strength copies for lols - at this point just about everything in advanced TFOs melts like snowballs in Hell anyway, so it really won't matter much unless you plan on running a lot of elites.