Its not about late-game designs, its about basic shipbuilding. You need to leave at least 1 free space on a ship (unless its absolutely impossible, but its a truly exotic case), as you will rise a speed by 1 then, that is a best use for 1 given point of space. You missed the Augmented engines and Inertial stablizer (must-be overall exept some early ships), and battle scanner (must-be for a beam ship, without it no need to use non-PD beams). While its possible to use F PD beams VS AI, due to total incapability of AI in a battle, its a bad habit still. PD should be 360, as your ships wouldnt be able to self-defence in case of missile heading from slightly wrong direction, and you will have a huge problem on concentrating the fire on missile during missile destroying maneuvers perfomed by a whole fleet. Its also quite handy to have Heavy beams as Fx, but it not really needed all the time, if fleet is really late and big - F is fine too, as you just shoot forward with it anyway. Normal beams are of low value generally, exept some special cases, say Plasma cannon, as they are of less range, and dissipate more on a given distance, compared to Heavy ones. By the same time PD modification is much more effective for a defence function, compared to Normal. Generally, the later game stage is, and more developed technology is used - the more important the beams become, very late ships could easily use only Heavy load (as you just inflicting heavy blow with one strike), while early one need a huge PD load with 1-2 Heavy beams.
More specifically: for a late beam ship, beside a real 100\125 computer one also want some overpowered techs - High Energy Focus, Structural Analyzer and Hyper-X capacitors (surely its possible to wreak havoc on AI without all the stuff).
Heavy armor - you can prefer HA over Rhull only versus AP weapons, that are pretty rare. Rhull, while offering same HP increase, also triple the Engine's HP, making the ship much more reliable and sustainable to damage. Also Rhull is important VS structure-damaging weapons, while HA simply have no effect at all in that case. Surely there is nothing bad at all to use them together, beside the space.
Autorepair - unlike moo1, where it is a good technology, moo2 autorepair is simply crap. Surely it can work versus AI, that is unable to concentrate fire on a ship and just randomly aim on some closest target, but using it is a distraction and a bad taste still. Goal is to prevent a damage to a ships at all, as much as possible, not autorepair them for a pretty large chunk of space (and that space is totally wasted, until the ship is actually damaged, so it just weaken the weaponload that time).
Weapon themselves is the least important here, but Death Rays are really weak weapon (compared to middle-late beams), and Lasers are simply better than Fusions for PD (you need to use all the mods, obviously).
In a summary - the certain ship have horrible low Beam Attack value for a beam ship (in classic moo2 - problem of actual beam ship is lack of good targeting computer, not actual beams, and good computers came really late), making it able to hit Starbases only on a regular basis (and probably some AI tin cans of worst designs too), have a weak damage payload, and basically non-existent missile defence capabilities. Surely would work versus Antares still.
