Regarding Ironclad vs Destroyer, I believe the game correctly represents the huge increase in lethality that world war tech brought about.
If there should be any change, it would be to introduce Cruisers to the game.
I suggest the current Destroyer is simply renamed Cruiser, and that a Destroyer unit with Strength 20 is introduced at the same time as Battleship.
Thus you have:
Cruiser (Str 30) comes first;
Destroyer (Str 20) and Battleship (Str 40) comes slightly later.
The Destroyer should obviously have certain advantages:
1) Make destroyers fairly cheap compared to costly Cruisers/Battleships.
2) Make Frigates upgrade to Destroyer
in addition to Cruiser. Not only does this answer the complaint that Age of Sail units are too expensive to upgrade, it also nicely carves out a brief era where Cruisers rule, but then encourages a shift from WWI-style navies to WWII-style ones.
3) Cruisers and Battleships (and Carriers) are to remain useless vs submarines
I think Destroyers should not be able to see subs until the tech that is concurrent with radar. The idea is for subs to have a very short window of opportunity where they can reign supreme, but that they become massacred by (relatively cheap) Destroyers as soon as they can find them. In other words, the fact that I suggest that the price of the unit that finds (and thus kills) subs is lowered, is quite intentional. This is most easily emulated by postponing Destroyers until Battleships, hopefully (I haven't checked the tech tree) allowing Subs to be build before that, when only clueless Cruisers units are available for protection (=they can escort Transports, but they can't hunt down the subs).
At least until nuclear energy becomes available, but that's another unit and another discussion. 