Well sci is the class that honestly benefits the most from peng spam capability.
This I think hits the nail on the head. Pengs are probably the best torpedo you can chooses as a sci. It needs the least amount of skill points (something sci needs more than anyone else), it is easy to get, it is highly effective, it partially bypasses shields and you spare a tac BO-skill because you don't need HYT. I have already a build ready for the time when Pengs are fixed to replace my Quantums. But this only counts for sci ships not necessarily for sci captains.
SNB: Change it now and you have no chance to remove resistance/healing stacks. Making healing even stronger. Yes it might need a change but for now it is a necessary evil.
Sci Fleet: This I agree could need a little nerf. Either just lower the res value or maybe make it dependant on the caster and the receivers aux level. (eg: Caster has max aux you get 30% shield res, plus 0-30% shield res depending on the individual receivers aux level)
CPB/TB: Well I use them myself so might be biased but these two I don't think are OP. CPB I can understand could be a problem if you face a team of sci ships all using it at the same time... but you could say the same of escorts who focus fire and they can make a lot more dmg over time than CPB. Maybe some kind of resist to CPB might be a solution so you don't get hit with it over and over again. TB on the other hand I don't see as a problem at all. The drain prevents a ship to regenerate shields without powers but on its own it is not that great. Both have the problem any shield heal counters them and in the end you still need the weapon power to kill the hull which sci lack most of the time. (By the way could it be that CPB/TB doesn't add to your dmg counter in PvP?)
Anyway I'm not really surprised that the new Peng and the fix of FaW leaded to more sci overall.
I could live with SNB just removing buffs. But the buff removal needs to stay as long as buffs are as strong as they are. And once they aren't, SNB will not feel that powerful either.
Charged Particle Burst is also only powerful because all other buffs are so strong. You can boost your damage up to the wazoo, hence you need to buff your resistance up the wazoo as well. Hence a power ignoring shield resistance is awesome.
In a way, Science is what even allows a semblance of balance currently, otherwise it would just be indestructable ships against infinite damage. And we would probably learn the answer to an age-old question, but while it might be interesting from a philosophical persective, it doesn't make good gameplay.