The Special Naval Technologies are cool and an interesting concept for the Themistocles at sea levels.

My only complaint is that while it is expensive to get the technologies, getting say all the Galley-Line boosting techs essentially makes elite galley's shred everything including buildings.

In Raise the Sails, I bought all of the techs for the achievement but the Elite Galley's were so overpowered I didn't even bother experimenting with other ships such as the sea wall option on destroyed Lemboi. I should add the navy starts off weak and progressively gets stronger, but one of the things the AI did on moderate was steamroll into Towers/Castles so I got the naval experience for destroying ships rather quick. Maybe don't have Aeginta (Purple) send ships to attack the fort protecting the main harbor the entire time. As for the coastal mine, thats a defeat trigger so the Pirates and Aeginta attack it consistently. The Sea Towers help big time in the beginning.

I think some of the techs could be interesting on a future civ or as shipyard technology and while I do think there is potential, letting all of the be researched in Battle of Salamis and Raise the Sails eventually leads to significant powercreep.

The other major water combat level I did that used extensive ships was Earth and Water, and while the Persians have a strong navy, its still tedious in the beginning until you get the ball rolling and take down Naxos (Red) which seems to be the most aggressive and strongest enemy in Earth and Water. And not having access to the cumulative effect of the special naval technologies makes the level harder.

Also I would also add that I check the stats of the enemy units to see what upgrades the AI gets and in some campaign missions, the AI will be in Imperial Age for a long time but doesn't fully upgrade their ships on water maps or land units.