You get marginal, almost useless gains from Tier 1 to Tier 5; such that you'd be better off researching better weapons.
Marginal? The difference between having a utility module and not having a utility module is huge. Much of the power of ships come from different utility modules interacting with one another. Many utility modules only provide a per-ship bonus, so a ship that has both an attack and a utility module is better than one without a slot for utility modules.
Let's look at each Tier compared to the one before it.
Tier 2 gets utility modules. This is absolutely huge; a fleet without utility modules is basically at the mercy of whatever the enemy brought. Utility modules can provide the flexibility to deal with a specialized fleet and even overpower defenses meant for you.
Tier 3 allows you to combine utility modules with a ship that can actually have a defense module. So now, you start seeing utility modules that provide bonus defense to that ship. This again provides a degree of defensive flexibility.
Tier 4's ability to combine multiple utility modules on the same ship means that you can boost a particular kind of attack to previously unreachable ranges. Alternatively, you can use the extra module space for larger modules; 2 slots might be the standard cost for global ship bonuses.
Tier 5 starts to bring multiple attack or defensive systems. However, none of them have utility modules, so you're still relying on older designs to provide additional bonuses to those systems.
Tier 6 brings the first 3 utility module ship. That should be pretty important, as you're now talking about the ability to have fewer ships with utility modules while still getting the same effect. You no longer have to rely on giving most of your ships utility modules; you can concentrate them in a few ships while the majority focus on having more attack modules.
Tier 7 gets you to 3 attack or defense modules. 3 attack modules can allow for a powerful 3-slot attack weapon, or just a lot of independent weapon systems built into an single ship.
You're thinking too much in terms of GC2's combat model, where attack and defense are the important things and utility modules just provide a small buff here and there. This system is designed around utility modules; the attack/defense modules are just something for the utility modules to key off of.
It would also be more likely to trigger an attack bonus based on type. Multitype weapons would not be so obviously inferior to single type, as you clearly stated later in your post.
That is the point. It is not a linear progression. New things are not automatically better than the old. And if they are better, they can be better in ways that don't matter to you right now. If your entire strategy for your combat fleets is based on buffing weapons based on "light" and "ion" types, a plain old "energy" weapon isn't useful for you. However, if your enemy has adapted, and they're using defenses based on "light" and "ion" types, then that plain old "energy" weapon is starting to look at lot better. It might actually do some damage, unlike your current weapon systems.
will result in massive module stacking to make up for the glaring lack of weapons.
How? Even the ship with the most utility modules only can have 3. There won't be any massive stacking of anything because the slot system forbids it.
Explain to me what the difference is between having four ships, each with a module that adds +2 attack to another's attack are functionally different from having four ships with a second weapon on them to add +2 to their own attack?
Because weapons shouldn't work that way.
One of the reasons for limiting the space for adding this is so that a weapon can be something more than just a number. Under my system, multiple weapon systems are not added together to get a single attack value. That is unworkable with a system that's built around bonuses against damage types because the types will all add together. Each weapon, even weapons on the same ship, attacks individually. Of course, each defense defends individually as well; a ship will use the most advantageous defense against each attack that targets it.
When I said I didn't like "bigger number wins," I meant it. This combat system is not built around bigger numbers, but smarter fleet construction. So you can't just win by piling on more and more stuff; you have to think about what you're sending into battle.
It creates much of the complexity of tactica combat, but it put it where it belongs: outside of battle.
This entire system strikes me as unnecessarily complicated and an AI programming disaster.
The AI for it may be difficult, but it's not that hard. It's all about reading what the enemy is using in their fleets and designing an appropriate counter. The last part is quite algorithmic once you know what your enemy is using against you.
why not just use the Sins system, with weapons that are more or less effective against different ship types?
Because then there wouldn't be ship design. This system is like putting together a Magic: the Gathering deck. You have to think about each individual piece and how it interacts with the whole.
The "Sins system" is limited and limiting. It keeps out player expression of ideas, in place of a forced dominance by the game designer. My system is about giving the player meaningful choices, while simultaneously forcing them to build exploitable weaknesses into their fleets. No fleet can ever be unbeatable; if you try to build a generic fleet, a highly-specialized one with overlapping bonuses can kill you. Highly-specialized fleets are themselves vulnerable to some particular weakness, so a well-designed fleet can counter them.