Your aurora problems overlook the fact Aeon has blaze and flare to address weaknesses of aurora when the weaknesses are too large for the strength. Your aurora suggestions are just normalizing the factions for no pertinent reason since Aeon t1-early t2 stage is hardly a problem.
Your t2 air diagnosis is just wrong, janus is not the most OP t2 air unit. Aeon has the best t2 air roster due to the sheer flexibility of their gunship in combination with all the mass concentration advantages janus brings in fighting air fights via swift wind. Corsairs and Notha across a large distribution of games are each capable of ending games in way more flexible ways than janus which will always require at least 6-8 prior to doing relevant damage. Especially since a janus play will always revolve around powerlocking, notha or corsair can simply bleed you by killing mexes which janus are pretty terrible at killing. Likewise they can go for ACUs.
Aeon gun was insane, two players can play exactly the same and Aeon will win with an ACU that has half HP. The gun existed as a solution when neither flare nor blaze solved the problem of aurora and Aeon t2 stage was using Asylums to keep aurora alive until you could harb rush.
Sub gameplay is just totally not based in reality. Early frigs don't care about subs because they kill BP in the water. You kill the frig, I just killed 50% of your bp, now I will have even more frigs which spread across the map which give me intel, passive AA damage, and kill your expansions. So long as frigates are the designated AA/Radar/HP of navy, they will basically always dominate subs in importance. Particularly since 6 t1 engies can emergency build a t1 torp launcher and halt any damage to BP that a sub could possibly do, can't do that against a frigate.
Giving UEF destro strong torp defense is a terrible idea just because cooper exists. Your suggestion is once against an uncreative normalization of factions rather than playing into the fact UEF has the most unit-mix centered navy of the 4 factions in T2 stage.
Your battleship analysis is just wrong, UEF BS is only going to get good at large quantities. This is just a commonly held opinion. Aeon BS is considered the best BS across maps just because it's rare to get senton style maps where you see 8+ battleships fighting each other. Aeon is the best in small quantities, especially in combination with a push leveraging their strong destro.
Aircraft carriers are good, they are huge HP for mass and give good AA. Include some aircraft carriers with some torp defense and torpaggedon has a real pain dealing with anything. Aircraft carriers are also much better at dealing with gunships thanks to the HP and range compared to cruisers, which are a common counter to deal with navy without losing mass in torps to random aa.
The destro stuff is just whatever. I had a game once where Yudi would keep microing his sera destros and passively building up numbers while repairing via resto field against Farm who kept making salems. At some point it was like 8 salems against 3 phim destros and they still couldn't manage to kill 1 of the destros because he would dodge enough damage that the regen + vet would keep the destros going. At some point Yudi matched the destro count and ran Farm over. This was on flood tabula too, not even a wide open navy map.
Aeon destro is a one-unit-does-all button that is harder to dodge than salem. It is better.