I would actually say it would be cool to place one upgrade slot on the cruisers. I think when you have an enemy with 20 cruisers you already know what to expect. What if those cruisers have upgrades instead? Let's say 10 have armour/shields boost and the others weapons boost would be a lot cooler. 1 slot would be not enough to break balances but would add a lot to the game variety.

btw to be clear I mean same upgrades we already have for capital ships, just 1 slot though

BTW since Im offtopic ing, it's true i also think there is big gap between the caps and cruisers, though im so used to it already..