I've just recently picked up my B'rel retro again, some helpful clanmates pointed me in the direction of the tricobalts, also recommended Bioneurals. I've been tweaking the design so I'll post what I currently have before asking my questions;
Reman Prototype Shields
Honor Guard Deflector
(To be Honor Guard Engine, right now Supercooled)
Attack Pattern Omega 3
Beam Overload 3
Torp High Yield 2
Tac Team 1
Aux to Struct 2
EPower Sheilds 2
EPower Engines 1
Tractor Beam 2
Polarize Hull 1
Transfer Shield Strength 2
Hazard Emitters 1
I tried speccing out less for knocking over cruisers and more for hunting down other escorts, especially those pesky Tac Retrofits. Tractor beam was therefore a must, and I took some more supporty abilities at the cost of extra damage output that really isn't that necessary against escorts. Beam Overload 3 usually can drop the shield facing for a Tricobalt HY2 to knock them out in one go, provided I have Attack Pattern Alpha, Omega, and Tac Team running (at least). The Bioneurals I find are very useful for either spooking them to pop buffs pre-pass, or finishing them off if my pass didn't succeed; I've have BNs chase not-so-bright escorts for a full half a minute before actually getting the kill.
Of all of this, Tractor Beam is definitely the center of the build. Stationary escorts are (usually) dead escorts.
Even though I doubt I'd implement it, as I like the way my Boffs rest at the moment (I can basically supercharge my shields if I'm coming out of cloak into a hotzone, polarize hull to slip out of tractor beams if Omega is on cooldown, hull repairs after I recloak and Hazard Emitters allows me to cloak through a Warp Plasma proc) a question more of curiosity; how do you get such high damage off Photonic Shockwave? I tried to run a DSSV transphasic boat fed-side with PSWIII but it never got close to that much damage.
My other question is basically timing; I typically decloak only when I'm within tractor beam range, hit the dual beams immediately, and drop the transphasic between 2-3K out while coming in at EPower Engines full-burn and APOmega running yet I've seen players within that split second pop up a run-killing tac team. Is there anything specific I should look for on the approach? Should I try to compress my timing even further if the tractor beam at 5km gives me away too early?
I used to run Tachyon Beam but I found even at an unbuffed aux power of 77 it didn't really do anything.
EmoeJoe Brel is very nasty and I often experienced it on my skin (it's an Italian way of saying!) at Ker'rat. He attacks you from behind decloaking and if your shields aren't at maximum you're dead.
So if I want to survive the flood of torpedoes and the trico bombing, if I'm lucky, I set a full power to shields and my double EPtS are always running, but since he can choose the right moment to attack, I'm prepared to weaken my assailant with an APD, while with a special keybind all my defensive buffs are activated.
But EmoeJoe, also Zirac and above all that damned Romulan (hi Star Dagger, you're the best!), well, they are too strong for me...