How about making the stock super weapon available midgame but do mediocre damage and have no secondary effects. Add research and upgrade modules to the super weapon to increase damage and have more secondary effects. This way you could make the stock weapon only threatening if you don't counter it but a fully upgraded weapon would be pretty scary.
Eg for Novalith
Out of box damage would be 750 per shot, no secondary effects. Could upgrade damage to 1500 -> 3000 per shot. Secondary effects could be loss of part or all tradeport income, slow pop growth, damage to trade ports, buff for friendly forces in grav well. You could still protect your planet with aux government , but the economic effects of a fully upgraded cannon would be severe, and it would make it marginally easier for an attacking fleet to overpower the defenders.
