beam fire at will is the same as spread, alot of aoe dmg at the expense of single target dps. try it and see how you like, but i don't think it'll beat BOL2, but then again i've been wrong before on these things.
The new tree looks much better than before. although i'd like to point out the 8 points in warpcore potential will only get you 1 more point in all subsystems as opposed to 6 point. personally i think the last 2 points can be better spent elsewhere. like some of of skills that boost sci ability like graviton generator.
So I noticed you took a few points out, and haven't reinvested them yet; and here's what I'd like to recommend...
If you are planning on using AP weapons as you main sourse of dps (and it sounds like that's the route you're taking), consider droping the last 3 points out of projectiles, and (with the extra points you already have) put it all in targeting system. The reason I say this is any accuracy you have that goeas over the target's defense gets converted to crit severity, so it is never wasted. And given that you're main sourse of dps comes from 5 energy weapons (AP, meaning high crits), you can probably afford use 6/9 in projectile skill.
As for the last 2 skill, it's something like +.5% crit and 10% severity (9/9 vs 6/9) so it's not really important at all. And I'm not sure what the exact numbers were, but it's pretty low.
Front Weapons: 2x Polaron Dual Beam Bank, 1x Quantum Torpedo
Aft: 2x Polaron Turrets, 1x Chroniton Mine Launcher
Deflector: Jem'Hadar (Assimilated alternatively)
Engines: Jem'Hadar (M.A.C.O. OR Assimilated alternatively)
(The Jem'Hadar 2 Piece set bonus gives bonus damage to Polaron weapons. Some say it's junk, but I'm still testing it out to see if the damage boost is really worth it)
Eng: Neuritrino Armor, EPS
Science: Assimilate, Abaltive Gen, Field Gen, Particle Gen
Tact: 2x Polaron Amps
I've been using it for a while now, and it seems to do decent DPS and the science skills are incredibly strong. However, it does lean more to the debuffer/crowd control role.
With this build, my Gravity well ticks for about 1500-1800. Beams do between 75-100 when shields are up 400-600 when iIm hitting the hull.
Im wondering why you went for Gravity Well rather than Tyken's rift if you are using Polaron. Tyken's III with high Auxiliary is almost a guaranteed drop of shields. On the minute cooldown, you got Polaron and Target Subsystems Shields to bring down the shields again. What is your opinion on Photonic Shockwave? I used it briefly, but it didnt seem to do much, and I had to get really close. And also Charged Particle Burst. Isnt that just a decloak and Tachyon Beam?
I use that build mostly for STFs. I like Gravity Well for the slows and crowd control. Same for Photonic Shockwave, it helps to push ships away from the Kang on Cure for example. I do have a spare B. Off with Rift that i switch in for PVP or if I don't have a retarded STF group, however.
Charged Particle I found is a bit stronger than Tach Beam, or can be if you spec for it and use particle generator console, the down side is that you have to be close to your target for it to be effective. With my playstyle though, I like to get in close. So I chose CPB over Tach Beam.
Charged Particle and Photonic also help give me some breathing room for when I get surrounded. You can also use Photonic to push enemies back into the gravity well or into ships about to explode.