Thats disgusting

. But more to the point, do you see any weaknesses in the current system?
The only way a command ship survives against Steel Reign is if it's built something like the following:
1 Twist Drive
5 DHe Fusion Core (Refined)
4 Deuterium Drive
1 Command Deck
1 Command Staff
1 Computer Module
1 Commlinks
1 Scanners
6 Jammers
4 EW Broadcasters
1 Gas Vents
9 Coilgun (Refined)
1 Lubricants
1 Barrel Casings
1 Pebble Net
9 Carbon Armor (Refined)
3 Tungsten Armor
1 Heavy Cladding
Cost: 311e (140e) / 69m / 103v / 0a / 0t / 103s
Size: 77 / Mass: 77 / IS: 1 / IP: 1
Range: 0 / Power: 8 / Heat: -5
Init: 4 (12) / Dodge: -21 / Avoid: 11 / Armor: 45 / Shield: 1
Refine: 522e / 131s
Projectile Gun Total Damage: 18
Init Bonus to Fleet: 8
Jammer Init Debuff: 5
Init 12 / Dodge -21 / Avoid 11 is enough to have Long FM Range hit chance down to 0%, which might enable Fleet Init Bonus to persist long enough for
Thunderbolt type vehicles to annihilate the
Skipjack types. Avoid 10 has a 1% hit chance (1.6 get through), but Avoid 9 has 15% (24 get through).
If the
Skipjacks are somehow in Short Range though, hit chance is 100% and this ship can still die; the loss of Init will cripple a high-dodge fleet enough (say, 10 Init / Dodge 6 / Avoid 6 down to 2 Init / Dodge 6 / Avoid 6) that hit chance goes from 0% to 36% and they die. Alternately, if you get off an Init Debuff on this, you might also reduce Init enough for missiles to get through, though that's down to EW luck. On the other hand, a Particle Fleet will have a hard time punching through an armored command ship enough to kill it quickly, so you can just keep trying your luck.
Short of a very specialized counter Particle Fleet like that though, I think Steel Reign will smash quite a wide variety of things through sheer ridiculous distributed firepower. The resources are a bit of an Achilles heel, but everything has one. (Like how expensive this counter-command ship is.)
Right now, I think the Kinetic Lance is the top tier low-tech weapon, despite its heft, simply because it can get around all the stacked Armor and Shields someone cares to fit, and it takes a significant investment in Avoid,
and Init, if not also Dodge, to stop massed concentrations of them. Meanwhile, Interceptors become a total non-issue if you have enough Lances, as Steel Reign does. With T4 components you'll be able to get Lasers that just power through everything, but they can only hit one or a few things at a time and are sort of glass cannons. Meanwhile, Particle is restricted to slowly chipping at massed defense until more combat-oriented weapons appear (the Railguns and combat variants of the Mag Catapult will perhaps change this). A huge outlay of Kinetic Lances, on the other hand, distributes the firepower, has range, gets the damage in, and allows for very finely granulated allocation of firepower to multiple targets. Its dominance will decrease with time but at around T3 it seems like a really good bet, and moving into T4 and perhaps T5 should remain quite competitive.
Right now, at this Tech Level and with these budgets, I think Macross Missile Massacre is king, and Offense Is The Best Defense.