So I've been thinking on the topic of some bonus ships being underwhelming, the difficulty of making high cap ships useful, or making low cap ships useful without heavy-handed immunities (such as to insta-kill), and similar issues relating to how combat is balanced. Keeping in mind AIW needs to actually be able to run on reasonable hardware, and players actually need to be able to comprehend how combat actually works, I've got a few ideas rattling around.
Armor (modified)
This topic has come up again and again, it overall I think a lot of people aren't satisfied with the current mechanic. It seems ok until you actually look at the ships and start realizing what the Mark system does to it. Worse, there isn't a solution to the Mark problem with how armor currently works. In addition, tracking not only armor values of ships, but armor piercing is mentally cumbersome. Effectively most players simply remember "oh, this guy has some armor and this guy is good verse armor" even when armor values can vary greatly.
Solution: Armor becomes a flat -50% damage taken. Units that ignore armor (aka, have armor piercing) do not have their damage halved. Units that strip armor remove the armor property for a period of time (that could be the difference between Autopods and Armor Rotters: Autopods are -armor for 2 seconds, Armor Rotters are -armor for 20 seconds). Armor can even scale up, with "Heavy" Armor reducing damage by 75%, and possibly some insane armor on something like a Mothership being -7/8ths damage. Armor stripping could work in a few different ways for stacked armor, but that's a detail that can be considered later. In the end, armored ships become simple to understand quickly. They take half damage unless something counters armor. Done.
The Mark Problem: Since damage increases greatly with ship Mark, when a Mark I with armor fights another Mark I, things work okay. But when a Mark I with armor fights a Mark II, that Mark II preforms MUCH better than normal because its DPS increases by more than the normal 100%. And it works the same in reverse. In fact, an armored ship with a greater mark than its target outperforms on two fronts and those two advantage multiply together in fleet battles.
Evasion (new)
This ability causes every other attack to automatically miss. Each attack flips a flag and the resulting value indicates whether it is a hit or miss. Shots that ignore evasion don't change the status of the evasion flag. Some ships could even have improved evasion, causing 3 out of every 4 attacks to miss. Mirroring armor, the option could exist for some crazy ship against which 7 out of 8 attacks miss. Most AOE damage cannot miss and so ignores evasion.
Shields (new)
This ability functions like an additional set of health. Unlike health, it is applied in Layers and listed as "Shields: 100x4" much like attacks. Damage to a ship is subtracted from shields first (and internally a ship with 100x4 shields is tracked as having 400 shields). Every 20 seconds every ship gets one layer replaced. So a ship with 100x4 that has 175 damage against its shields would conceptually go from 100+100+25+0 shields remaining to 100+100+100+0 shields. In effect layers act as the regeneration rate. An additional advantage of shields is bonus attack effects do not apply against shields (e.g., reclaim, sabotage and engine damage is ignored). A disadvantage of shields is any unit that ignore Force Fields also ignores shields. Attacks with "Shield Breaker" always completely destroys any partially damaged layer after dealing damage. So 105 damage with Shield Breaker would take out two layers of a 100x4 Shield.
Unit Size vs Weapon Size (new)
All units have a size right now, but it isn't codified into a player-friendly chart. So assign each unit a size from Micro (1) to Colossal (8). Next assign each weapon a similar size. So a Fighter might be Size: Medium (4) and its ammo might be Medium Shells. Whenever one unit attacks another, it deals 20% less damage for each size difference between its weapon and the target, in either direction (dmgMult = |hull.size - ammo.size|^0.8). So an Artillery Golem with its Colossal Artillery ammo deals a lot less damage to a Medium Fighter than a Massive Armored Golem. Of course its base damage is so high it still erases the Fighter. If every unit in the game used weapons the same size as the unit, this would not change match up results at all (because if I'm doing less to them, they would be doing less to me). But this does leave room for units mounting larger or smaller weapons to specifically make them better against a different sized opponent.
Additional, the Point Defense ability allows a ship's ammo size to count up to two sizes smaller, allowing for 100% damage against targets that are 1 or 2 sizes smaller than its ammo.