I'm flying a Recon Vesta with a Sci Captain in a full sci build (heavy on debuff). I'm currently using the full Jem'Hadar set with a full Breen set on a backup ship (a Chimera) because the Jem'Hadar set has better overall stats for a debuffing sci build.
I've got bits of the Reman set, a couple of both Borg sets, progress toward Nukara, and I'm wondering which rep I should be focusing on. Is there a consensus on which gear set is the "next step up" for a sci? This is assuming a support/dps PvE build for ESTFs.
The deflector is always the centerpiece for the sets, so find the deflector(s) that suit your ship type the best, and then make a second pass based on what is available. Generally speaking, the KHG [Adapted MACO] deflector is the best for offensive sci, due to the boosts in Particle Gens (exotic damage) and Subspace Decompiler (duration), however it doesnt have any defensive sci skill boosts at all. The other deflectors are mixed offense/defense or more defensive in nature, specifically the Omega is much more evenly distributed, and then you have the Jem'Hadar deflector is good for drain/hold/confuse, and Romulan/Reman boost hold offense and defense (only) to very high levels. So really you need to think about what you are doing with your ship, what kind of sci focuse you have, and then look at what is good to build around that.
Personally I luurrvv using the KHG/Adapted MACO on my sci captains, every ship they fly, without question. The KHG deflector has the best attributes for offensive sci, and the other pieces and set bonuses also complement common sci configurations as well--boosts to torpedo damage is nice because I cant afford to skill out projectiles very much, mask energy field gives me a shields-up fake battlecloak ability that also complements carrier-centric attack formations, and so forth.
I also like the Omega set for a more drain-oriented build. There are some interesting set bonuses on it too, the 3-piece boost to Kinetic can help with torpedoes as well as boost exotic [kinetic] damage from gravwell and such. I am developing some ideas for ships to use this set, but at the moment everything in my sci arsenal (including escorts that only use subnuke and sensor scan) only use the KHG sets
Standard disclaimer--of course you can also mix and match