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Here is my build as of 3/21/2015 the U.S.S. Exia Freedom.

I'm looking for some advice on how to increase ship damage output to be able to put up a decent fight in PvE while still enjoying my futuristic torpedoes flying. I'd like to keep the the bulk of my armaments transphasic weapons and all projectile weapons. I am also looking to increase my defenses . I'm completely open to any suggestions. 

A couple of things to note. While it may seem odd, I don't PvP often so it shouldn't be taken into account, and for some reason I can't figure out how to earn large amounts of EC making it difficult to obtain or upgrade certain items.
3 tac teams is 1 to many. 2 will assure you always have 1 on GCD so the 3rd is wasted. IIrc it will be the same for the 3 torp abilities, 1 TS starts 15 sec CD on both your other TS and THY. Not sure if you have these abilities on a spacebar KB but if you do 1 og the Torp ability will never get used

TacPaddy

I would also alter the BOFF settings. Replace one TT1 with THY1, the replace the TS2 and THY2 with APB1 and APD1. This gives you a bit off a flexibility.

You should also respec. This list will show you, that putting nine points in most skill is not worth it.
My recommendation, reallocate the 9 pts from Armor Reinforcements into Aux Performance (3 Points) and Weapon Performance (6 Points)
Drop Warp Core Potential in toal, because the Bonus is a pure joke. Put them in Warp Core Efficiency instead.
As for the remaining skills, I advise to liberate some pts and allocate them to Subsystem Repair and Power Insulators.
Thanks for the suggestions, I've made the modifications and am going to test them out soon. Anything else?
http://skillplanner.stoacademy.com/?buil...domv2_3155

I did some edits to your traits, boffs, skills and gear. I will not go into the skills too much, suffice to say a lot of things are useless on a pure-torp build such as Weapons power in addition to what TP has already addressed above. 

I picked out all of the traits I use on my torp builds, along with Space Rep powers that boost torpedo efficacy significantly. These will improve your shield penetration and cause your torps to do damage over time as well as increased base damage. 

GEAR: If you stick to transphasics, there are now two gear sets you can slot together to significantly improve torpedoes thanks to the recent holiday event. The Breen space set's 2-piece bonus offers a significant boost to transphasics, and the Adapted MACO space set 2-piece offers about 25% damage boost to all torps. Slotting these together along with your tac consoles will provide significant bonuses, although the AMACO bonus doesn't apply to the cluster torps since their damage actually comes from mines. I also dropped your plasma manifold as you don't need power on a torp ship. You should be running the bare minimum in weapons, as high as you can in Shields and Engines, and whatever's left in Aux in that order. Definitely stick with the heavy escort carrier as the torp console is awesome with 4 tac consoles boosting it along with your gear. I changed the pets to the Fleet Yellowstones, highly recommend these as they have excellent crowd-control abilities and are very durable in space. Get the elite variants if you can afford them. You'll notice I moved your cluster torpedoes to the left - this ensures they fire first. You want those to fire as soon as they're ready and weapons fire in order from left to right once their cycle is available. 

DOFFS: This is absolutely crucial - you need 3 projectile weapon officer doffs which cause your torpedoes' refire time to improve a few seconds on each torpedo fire. Get the purple ones if you can afford, the Nimbus episodes offer a free purple named Law and I think there are doff chains where you can get others for free. The way these work is that each time a torpedo-class weapon is fired, the doff has a chance to proc and cause the refire for ALL torpedoes to drop by 2s for the purples. This includes your cluster torps, so the refire for them drops from 30-45s down to a more manageable 10-15s. Each time you fire each doff has a chance to proc, and they can stack, so it is possible to have all 3 20% chances work on a single torp. This works great with photon torps and with the Rapid Reload transphasics since they have a 6s reload normally, firing very quickly. I also added two of the clusters up front and left one rear because that way you have a big punch no matter which facing is towards the enemy. Just keep in mind that the clusters can be shot down en route to target, so this build will work best flying up close and personal at speed. If you have the Risian doff from the summer event which allows Evasive Maneuvers to instantly recharge on use of Emergency Power to Engines, I'd suggest using that in your 4th doff slot and then changing out your EPtS for EPtE. The last doff can be whatever you want (or 2 doffs if you have your 6th space doff slot - you can buy these at the Embassy I believe). 

Boffs: I agree with the others above so I made some changes here. I prefer Torp Spread over Torp High Yield especially on this build since you've got the cluster torps. Torp Spread does not miss, unlike High Yield, so it will do more damage consistently and particularly in STFs where you're usually targeting groups. Cycle APO and APB as needed. I also dropped Photonic Officer as it is completely useless in practice. Polarize Hull will give you more damage resist and give you two alternating tractor beam immunities with APO in place as well. I'd also make sure to alternate usage of A2SIF and PH so that you can keep your damage resist high. 

This should be a significantly more effective build if you can work towards these changes. I've run something similar and was able to hold my own in the old ESTFs pre-DR, even Cure Space, and now that you can slot the Breen core and get 2 stacking space torp bonuses, this should be even better. 
I was unable to partake in the winter event... it kinda throws this all out of whack. Is there some kind of work around or substitute?
You can just use two pieces of the Breen space set and whatever you want for the warp core and 3rd space gear slot, then. The other Breen space gear set pieces are free through the Breen space episode series. You won't be able to run AMACO and Breen together though. It'll still be effective either way. Put an AMP core in there that has something like SArrowE, EArrowS, SArrowA, or EArrowA.
Thank you, you've been very helpful.  Live Long and Prosper
I found a few of my older torp builds, you can check these out for different ideas as well:

http://www.stoacademy.com/tools/skillpla...build_3155 Armitage build
http://www.stoacademy.com/tools/skillpla...build_3155 This is another transphasic build so it may be relevant for you. Listed with Mirror Escort but can use anything really. 
http://www.stoacademy.com/tools/skillpla...umari_3155 TP Kumari. This is a fun one because the Kumari moves fast and is a lot of fun to fly, but I could probably make this a lot better nowadays.
http://www.stoacademy.com/tools/skillpla...build_3155 Wells science vessel
http://www.stoacademy.com/tools/skillpla...pboat_3155 Blended torp and tetryon build on an Avenger - this one drains shields like crazy and then the torps hit
http://www.stoacademy.com/tools/skillpla...torps_3155 - Same type of tetryon/torp on a Defiant, this one with plasma torps

Finally here is one I've just completed that I have been working on:
http://www.stoacademy.com/tools/skillpla...pboat_3155
This uses torpedoes plus a lot of exotic damage via GW3/TBR to smash people into nothing.
Question? Can "Expose Weakness" be triggered by fighters? If not do you think adding two arc anti-proton beams and a kinetic cutting beam aft work?
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