Submarines should be more expensive than frigates. It's got to be more expensive to design a unit capable of submersion.
Submarines should be able to hunt enemy submarines. Perhaps you could reduce sonar range if you want to make sub warfare more of a cat-and-mouse game, but they definitely need to have it. Why even have subs if you can't have subs-hunting-subs?
I don't think we want to increase the defender's advantage for subs, because they're supposed to be offensive/raiding units.
Buffing UEF sub hp could mean that it takes 2 passes from a torpedo plane to kill which could totally unbalance the game. (You could fix this balance issue if you just made UEF t1 subs better than all other faction subs but also more expensive. i like this idea because I don't think we need all factions to have the same naval options. I wouldn't mind if UEF's sub game was different from that of other factions, as long as it was balanced fairly.)
How about: cybran sub torpedoes have an EMP weapon that only affects buildings. That would add a bit of "flavor" to the faction. If the stun was brief enough it wouldn't be OP. But it would help them to overwhelm static defense and to annoy shipyards.