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Here's an idea ..semi serious.
What if you had to choose between a Titan or superweapon at some point, and one canceled out the other?
Than everyone would choose the titan ship and the superweapon spam would be solved.
Or just add a toggle for limiting the numbers of/turning off super weapons.
Or just make the super weapons take up a cap ship slot and fleet capacity.
Not really a fair choice as you can get titans so much earlier. Really I think the superweapons are an AI problem, once its optimized for Rebellion I think the problem will largely disappear.