is there a cost effective counter for the t3 seraphim sub-hunter?
Torp bombers work well, as do aeon destroyers and uef coopers. Cybran t2 subs can also work.
Is the aeon experimental battleship ever worth building? It seems to be rather medicore in virtually everything compared to everything else for that cost. Same for the atlantis, is it worth it purely for the combat effectiveness, or should you treat it as an aircraft carrier?
Normal navy is usually better I think. The advantage of experimentals is that they build fast. In some cases the range on the aeon exp battleship cannon and on the atlantis torpedoes may be worth it. I don't think it's worth building an atlantis as an aircraft carrier. You're better off with air staging facilities.
What is the best way to try to reclaim a sea presence when you are pushed out of the water completely, or what is the best way to stall any shore damage for as long as possible for when that is not possible?
As cybran/uef you have great torp bombers that work even very close to the shore. As aeon/sera you should probably use hoverspam. Against cybran navy, and maybe against uef navy you can also build t3 gunships.
The non-uef destroyers seem to be pretty effective against both submarines and surface targets, is there actually a reason to build t2 subs during the t2 naval phase?
T2 subs, especially the cybran ones, are effective against sera t2 destroyers. Sheppard suggests that you mix subs with other navy. I disagree. The whole point of subs is to deny your enemy his surface dps. If you mix in other navy that surface dps just switches to other units, so you've accomplished nothing. If you do subs, you shouldn't mix it with surface navy, or you should keep that surface navy out of range (e.g. cruisers that are just present as anti air).