I expect very few people to respond to this after -
*checks watch*
- two months. Geeze.
VarroWayland Your designs are fairly solid, but for some reason you don't use engine rooms. You have lots of internal armor which doesn't do much good if the weapons are destroyed. 
Looking at the Trident, this bit right here has bad energy supply. The front is poorly armored, having essentially only two shields and pieces of corridor for protection. The side missile launchers have poor reload, and the ions have inefficient combination. You have a lot of PD on your ships that's going to be very crew-intensive to keep supplied. Also, the Trilobyte's EMP launcher has the crew trudge through quarters or energy supply to reload it.
Try sending your Trident Mk4 against one of these in an AI vs AI fight:
I_Am_Jarvis Your reactors chain, the Rook has no way to power some ammo factories and has an unnecessary amount of reactors, ammo factories. and FTL drives. The Rook's primary defense only applies to ships in front of it. The flaks have trouble piercing shields and are out ranged by every other weapon on a rather slow ship. Try fighting two of these with the Rook, AI vs AI fight.

Your Harbinger has unnecessary reactors, gratuitous use of conveyers, and exposed shields. Fight one of these AI vs AI. with it.

Minty_Kee2 You have a torpido (sic) factory routed through a shield generator, poor energy management (those lancers do not need a plasma generator to themselves, that's 2.5 excess power right there), you have enough factories to sustain 2 macro cannons, but a whole lot more macro cannons then that. Rear plasma generators are only protected by a shield. Also, no fire extinguishers. At all. the entire ship burns to death. Since you have changed accounts and have a modded ship, fight nothing.