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It'll be best if we knew what your Tactical and Engineering boffs were like so that choices can be made that synergise with those abilities. eg: At the moment we cannot assume that you have any sort of hull/shield healing/buffs on the engineering side. For all we know, you could have chosen EPtW and DEM, which then places the burden on the science powers for shield and hull heals.
It'll also be nice if we knew what you were planning on focusing on. Random missions/stuff where you'll most likely be in a solo situation; PVP; STFs etc...
If you intend to do both PvE and PvP, ideally you'll have multiple boff configurations to swap in to best suit the situation. Under normal mission play, you'll be perfectly fine so long as you have TSS, HE and EPtS. The real fun is in varying your payload for other stuff
Tachyon beam is a little iffy as a general purpose ability unless you're going to be cruising around in full aux and with flow capacitors since decent weapons fire would punch a hole through the shields faster. It is, however, great to drain the shields of a highly resistant target, such as will most likely be the case in PvP. Doffs can also add a turn rate debuff when using Tachyon Beam, which helps give it a little bit of extra utility. Tachyon Beam is a deflector ability, so it shares the system cool down with other abilities like Gravity Well, Tyken's and Energy Siphon, so keep that in mind
As you are using I'm assuming, a sci ship, you may want to consider getting higher ranks of Transfer Shield Strength. It is one of the better +resistance/healing abilities in the science arsenal. Rank 3 is trainable only by getting an commissioned officer with the ability, which normally means digging through the exchange.
Hazard emitters is great. A nice hull heal, +resistance and removes dot effects while it's active like plasma dots and the nasty borg shield neutraliser. It depends on how hard up you are for hull healing in which rank to get. If you grab Aux to SIF in the engineering Lt. slot, you can rely on that for general purpose hull healing and keep HE for special situations.
Science Team is generally used only for the debuff cleaning effect. The shield heal is somewhat mediocre and doesn't give any +resistance which is important as you fight more difficult encounters as it helps increase the effect of subsequent heals and your regen. You may wish to consider moving it down to the ensign slot.
On a similar note, Tactical Team is mainly used for the instant shield redistribution effect, so keeping it in the ensign slot allows you to have a more effective damage ability in the Lt. slot.
Tyken's Rift is an amazing ability and its useful in most situations. An AoE power drain is always welcome. I personally need to see if Gravity Well 3 is worth its place instead of Tyken 3 for the damage it can bring. I have no problems recommending it for the Commander ability spot under most situations.
Gravity Well is another amazing ability. AoE tractor, it can lock down groups of enemies for AoE punishment or simply prevent them from moving and buy some time.
Viral Matrix used to be awesome where it totally prevented the target from taking any action back in the day. I personally don't like random system shutdowns, but I suppose it's handy to have in a PvP situation where you may want to force a target to burn their Sci Team to then follow up with a sub nuc beam to lock them down. I'd much prefer the certainty of energy drains like a Tyken + Target Subsystem combo when it comes to taking a target out of the picture for a while.
You may want to consider abilities like Jam Targeting Sensors. In PvE it allows you to disengage from a target, speed away then regenerate/repair and refresh yourself for a re-engagement and can also help in PvP to force a break from an opponent and also prompt them to try to clear using Sci Team -> Sub Nuc chain.
I personally load one of my boffs with Sci Team I, HE II, TSS III and Tyken III and use that as the standard go-to boff. If I move that boff to the Lt.Commander spot, I still retain my three standard healing/defensive abilities and can slot in another commander boff for a fresh set of abilities as the situation demands it.
Polarize Hull I've found to be situational. If you know you're going to take burst damage, it's great to add a big chunk of resistance. It also prevents tractors from locking onto you. However, it doesn't have much use outside of this, so it depends on how often you'll get into a situation where you'll need it. It shares the same system cool down as Hazard Emitters, so it has the side-effect of locking out a hull healing ability at times where you may need it.
Energy Siphon in theory is better than Tyken's in a one on one situation since the target cannot run from it, and you gain the power. As mentioned before, it shares the system cool down with Tyken and Gravity well among other things, so its your decision if you want to keep it on.
Both Tyken and Viral Matrix only really become effective when you bump them up to the higher ranks. Tyken especially since that's an energy drain while VM gains additional duration for the subsystem shut downs. Gravity Well is perfectly fine at rank 1 and increasing ranks helps with its damage and I presume its pull effect/duration.
Really depends on what you use the most and what you prefer to have as the stronger ability. I would say Tyken and Gravity well are the stronger all purpose abilities as they are multi-targeting.
instead of tractor beam or repulsor (your call) I'd make sure to get a Charged Particle Burst in there. It comes in really handy as a One-Two punch to take out small fighters, drones, removing the last shred of shields before you use Photonic Shockwave.
Personally, I recently restocked Feedback too. More hull damage vs things that fly really fast to go along with Tyken's and/or Gravity Well.