I don't have a Fleet Reconnaissance Science Vessel yet, but I will when my starbase gets a Tier 2 shipyard. I am using the normal Recon Sci vessel now.
This is a "tackling" build. Tackling is a term used in some MMO's that refers to incapacitating an enemy without killing them. I think this build gets pretty close to doing that. If set up right, you can hold an enemy in place, strip off their shields, keep them from turning, and shut their subsystems down. Then you can pick them apart with torps at your leisure.
It has two copies of Tractor Beam, Tachyon Beam, and Viral Matrix. When fully upgraded you can use Tractor Beam and Tachyon Beam every 15 seconds, and Viral Matrix every 30 seconds.
My suggested equipment loadout is as follows:
Fore Weapons: 2 Tetryon Dual Beam Bank with [Acc] and [Dmg] modifiers, Quantum Torpedo Launcher with [Acc]x3
Rear Weapons: 3 Tetryon Turret with [Acc] and [Dmg] modifiers
Omega Force Deflector
Omega Force Shield
Engineering Consoles: Assimilated Module, Neutronium Plating
Science Consoles: 2 Flow Capacitor, 2 Field Generator
Tactical Consoles: 4 Zero Point Module (currently limited to 3, on normal Recon Science)
Please note my ground skills are set up for the Medic Kit. I think I should change the 5 points in Physiology to 3 points in Willpower, but you may want to use a different kit and different ground setup anyway.
This setup has only one heal - Sci Team, (tac team doesn't really qualify as a heal) so its a little vulnerable. But whatever you attack shouldn't even be able to put up much of a fight. This build SLAYS bosses in PvE. It also works great on Khitomer Accord Space, as you can shut one probe down with Viral Matrix and then grab another with Tractor Beam and take it out quickly.
I run with my power levels at 25 weapons, 75 shields, 25 engine, and 75 auxiliary. Emergency Power to Aux and Emergency Power to Shields sends them both over 100.
In PvP you may want to expect varied results. It can be effectively countered with Engineering Team and Polarize Hull. You could still screw someone up for a short while if you opened with Subnucleonic Beam, but that skill has a 3 minute cooldown.