Make them more useful in sieges. At the present, if you have a siege with no biremes but plenty of fireships, and the siege gets hit by nuke that is not equal to or greater than the number of fire-ships present, the siege will die. I no longer have the screenshots to prove this, but I've seen it happen.
They also can't stop a CS from landing in a snipe. This should be fixed.
The integrity of their defensive prowess is undermined by people who attack with biremes as a cheaper means of killing off the fireships. A few well timed birmes after a lightship nuke or two ensures you kill all fire ships with minimal losses to your troops. Fireships should be the first defensive line, imo.
If nothing else, the unit should be scraped, or live on symbolically through the tower to give players a clearer understanding that the tower also gives naval units a defense boost, not just lands. Many players who are vets of more than one year are still subject to learning that tower affects both navy and land.