ImNotLaffng Balance them more by:
Making the factories require a lot of energy, missiles AND a new thing produced in the factory called "uranium" and make sure uranium and nuke missiles are slow to produce.
In more detail:
You need to have an ammo factory, a missile factory, an energy source, a uranium refinery (3x3 size), and a nuclear weapons production plant (4x4). First, you need to power up everything with energy. Next, you produce missiles. You then insert ammo (assuming that the cosmoteer ammo uses uranium for density) and the energy turns the ammo into uranium which is a slow process. Then, you place the uranium into the nuclear weapons production plant, add the missiles and energy, and after a short time, nuclear weapons.
For a single missile, should take about one minute to produce.