It can't swim

No seriously use BI.exe, which I've found will work with saved games.

In my marathon Roman campaign, I had a ding dong naval war with Carthage, they kept re-invading Sardinia, but currently I've had to raise several Quinqeremes to sweep the Ptoly navy who are considerably the biggest navy around and very powerful ships.

Whilst it doesn't make naval warfare as complex and subtle as it was, it certainly stops it being an after thought, if you don't build fleets the AI can spring some nasty suprises.