I am a SCI captain currently running a MMRE -- really happy with the ship btw. I am fairly pleased with my spec currently, primarily focused on crowd control, but feel that my sci BOFF skills aren't quite what I need them to be.
My set up is MKXII MACO set. 3x phased polaron DHC up front, 2x phased polaron turrets in back and the Borg cutting beam.
Generally speaking, if you want a science vessel to contribute well in all aspects of PvE ( and I stress PvE, as many more sci skills are borkedin PvP), you're better off rolling a torpedo boat. Of course, this is just my opinion, but it's been my experience that even Vestas benefit best from using torpedoes. My Nebulas build will differ a bit from yours, as not only is the ship most stout than the MMRE, but I'm an engineering captain to boot. I can afford to take some risks:
Eng: Neut Armor Mk XI (R), Vent Theta, Isometric, Graviton Pulse
Sci: Field Gen MkXII (VR), 2x PartGen MkXI (VR), Zero-Point Console
Tac: 2x Plasma Torp dmg
So, what I am able to do is throw out two hull heals, one shield heal, have a great deal amount of CC/dmg (upwards of 7k dps), while still tanking very, very well. It helps that you can cycle through sci powers faster with Aux2Bat, and in a pinch you can pop an aux battery to counter the power's effect. Most of the time I'm running around with max defense and aux power, and my grav well is usually only 25-30s away from its next use. In the heat of battle, I can constantly throw out GW3, which is of infinite use on CSE and KSE.
Again, I'm an engi captain, so I can make use of my career skills to help me tank and keep power levels where they should be. Since running energy weapons means taking power from Aux and Def, which you don't want to do as a science vessel, I again stress the viability of a torpedo boat. Roll with two VR projectile weapons and three VR technician doffs, and you'll do just fine.
But....as to your original question, there are very few powers worth having as a science captain. Repulsors are okay, but their damage isn't good enough on regular targets (i.e., moving) to warrant always having. When I ran with TBR3, I found myself having to refrain from using them, lest I move a valuable target for my allies out of the way. And this is with no points into GravGen and 4 into aux. TBR3 simply cannot be used as a good replacement for the now-ubernerfed PSW3.
GW3 and TR3 are good to use, but you're best off picking one due to the shared cd. And while TR3 is nice, and synergizes well with tetryon/polaron drain builds, I'd rather have the guaranteed slow from GW3. Plus, more damage from my experience. Siphon is decent enough to carry as a slight boost to power levels, but don't expect it do anything phenomenal. It's best left to the lower levels as a throwaway power if you need it. And again, drain builds are able to work, but better on the KDF side.
TB3, PSW3 are worthless, but Feedback Pulse 3 is quite hilarious when buffed, and FbP2 is a good power to have when under fire. It won't contribute too much to your damage, but if you don't like TSS, then I don't think you'll be wanting a higher power of that to put in the Lt. Comm spot. I'm not a big fan of making a science vessel so tactically-minded over staying alive, but if I were you, I'd run this: