The AA gun thing doesn’t bother me, it is a unit and if they want to give it to me as I stomp Moscow so be it. I can see how it could do more then delay in some rare cases. Like your ally not being able to clear a tt with air only for you, but that’s a good strat on there side.
Subs not soaking up air hits w/o enemy DD took a while to get used to. This situation normally comes up early in the game when UK attacks Germany in sz 5. Unless you add to that fleet your going to loose it any way. With your sub(s) not being in the battle at least you get to keep it(them). Try adding a sub or two in your 1st turn (Germany) then you may have a counter attack with your air & subs at some point. Germany can’t normally build fleet with UK but subs/air are a cheep way to harass the British and keep them honest. By not being able to throw your subs away early, may help you later.
I do have issues with transports floating through hostel waters containing subs only. The whole point of the defenseless transport rule was to force you to protect them. This is the exact opposite. We have house ruled this in our group also. At the sub(s) option we allow the subs 1 roll each (attack roll) on the surface fleet as it passes over. The fleet also gets a roll at the subs (a defensive roll). This doesn’t stop movement and only last 1 cycle. The subs wouldn’t normally take this option against a larger fleet but they should be able to attack a weekly defended fleet w/transports in my book. Keep the enemy honest. We also use a sub detection rule so one DD doesn’t see all subs. Sorry kinda got off topic.