If you are going to restrict the ships to the same weapons irrespective of their sizes then I agree that larger ships are generally better since they can carry more weapons.
However, if the different ships carry different weapons and are designed to different requirements, then the outcome can be very different.
I acknowledge in advance that these designs are at the extremes of what you can do with the system
Ship One - "The Death Star" (2055)
Hull: 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1
Engines: [TL0] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Shields: [TL0] 5 5 5 5 5 5 4 4 4 4 4 4 3 3 3 3 3 3 2 2 2 2 2 2 1 1 1 1 1 1
Weapons: [TL0] 1:[V] 2:[] 3:[] 4:[] 5:[] 6:[]
Battery V: Ship Killer, 10/20/30, 1/2+/6/6, Extra Hull Damage; Ignores Shields; Starship Exclusive
[G]
Special: [TL0] Overthrusters; Carrier (150)
Fighters: [TL0]
3xFighter, 6/10/0, (Fighter/5+)
Ship Two - "The Stinger" (42)
Hull: 1
Engines: [TL0] 6
Shields: [TL0] 0
Weapons: [TL0] 1:[4V] 2:[4V] 3:[4V] 4:[4V] 5:[4V] 6:[4V]
Battery V: Sting, 1/2/-, 1/2+/1/1, Carronade; Ignores Shields
[AB] [AB] [AB] [AB]
Special: [TL0] Stealth; Carrier (12)
Fighters: [TL0]
1xDart, 6/6/0, (Seeker/5+)
Ship One will destroy any ship it hits but it only has one weapon so it can only destroy one ship per turn. I have given it Overthrusters to compensate for the low engine rating and limited weapon arc, but you could change this for Armour Plating, Fire Control or Countermeasures. It has a few fighters as it had a bit of space left after putting in the super-gun - they at least give you a bit more flexibility.
Ship Two makes use of knowing what Ship One can do in order to design a countermeasure to it. Ship One ignores shields, so don't bother with them. Ship One has a very long range weapon, so use stealth to reduce the effectiveness of that. Ship One has a high shield rating, so select a weapon that ignores that. The seekers are almost an afterthought but may be useful against the fighters, or you could take countermeasures or point defense instead.
You can get almost 49 Ship Two's for the cost of a single Ship One, more if you tweak the options a bit. As Ship One can only take out a single target each turn quite a few Ship Two's will survive to range 1 where they will gradually nibble away at the "supership". In fact I suspect that the real issue for Ship One is not taking Hull hits but taking that one weapon hit that will leave it as nothing more than a giant target (18 successful hits should do that I beleve which with four shots per attacker won't take long to do).
I know that these are rather extreme and purpose designed ships (although I have seen similar suggested as serious vessels in the past) but it shows what you can do within the rules to bring down those giant ships.
