AI War was a masterpiece, there's no denying that, but an issue that has come up again and again over the years is the problem of hull types, and countless discussions on how to balance them.
At first it wasn't a big deal, because there were so few ships in the game that hull types were easy to balance, but as the number of the ships in the game doubled, then tripled, and quadrupled, the entire system became one giant mess, which was constantly having to be "rebalanced" (If you remember Keith doing the "worst ship in the game" polls every week), which was more of a band-aid than an actual solution to the problem.
Another problem with the hull types is that was unfriendly to new players. AI War is complicated enough as it is, and has a steep learning curve in a world of increasingly impatient gamers, having them memorize the hull types of hundreds and hundreds of ships, and also the modifiers of each ship is honestly too much to ask, even of the veteran players.
The third problem is that it's forced design. Fighters don't do extra damage to bombers because they're faster, or because they can dodge the bombers' attacks, it's simply because there's a modifier that says they can. Missile frigates don't beat smaller ships because they have numerous small attacks (like something you would see in a mecha anime or sci-fi movie) -- missiles that break into yet smaller projectiles that seek out fast-moving ships, but are fairly ineffective against big targets. No, it's because they have a modifier that says they are good against fighters. That's it.
The truth is, you could make the game's ship balance intuitive. Everybody already knows that fighters beat bombers. Everyone already knows that frigates firing massive amounts of tiny missiles are going to beat strikecraft. You don't need to add hull modifiers to make this happen, all of this can be accomplished with a very simple armor system, and basic stats like damage, penetration, and number of projectiles.
Every ship in the game could be balanced in this way. Fighters beat bombers because their DPS is significantly higher, because they are cheaper, and because bombers have huge frontloaded damage that fires infrequently, where fighters are very numerous and can simply overwhelm them. Bombers beat Frigates because Frigates fire tons of tiny rockets which the bomber armor can absorb, and because Frigates are less numerous than fighters, and thus are very vulnerable to the Bomber's frontloaded damage attacks. Fighters are vulnerable to Frigates because they have no armor, and because the endless volley of tiny missiles overcomes their superior numbers.
All the counters still exist, but in a much more natural way. It's a way that any player who has watched a sci-fi flick ever will instantly understand, the learning curve is much smoother, and every bonus ship in the game can be balanced using these same simple principles.
In the end, the hull type system will never be balanced. Certain bonuses are always going to be more important than others simply because of the nature of the game, and certain hull types are going to be more favorable because they are countered by the least amount of units. In the end, the more ships you add to the game, the more of a balance disaster it becomes, and the more difficult it becomes for new players to try and memorize all the types, and all the modifiers of each ship. I think nearly 10 years of iterative design has proven this.
For the sake of your new players, and for the long-term quality of the game, I highly suggest removing this forced design mechanic, and replacing it with something much more organic.