Personally I wouldn't change the "nuke behavior" of the subs. I think it is nice the way it is (even though I understand the logic behind this proposition).
I would only make the tml play a more active role in the gameplay. Today, they are almost exclusively used for nuke purposes, people always disable their tml ability to keep them stealth (making their tml obviously useless). I wouldn't see this change as making the sub more powerful as you would either use the sub for nuke launch (in this case you would reasonably not use the tml to keep the stealth behavior), or you would use it as a tml platform, never both for all practical purposes.
I believe this enhancement could really be beneficial: it would give you a choice in using your t3 subs: surprize nuke or sneaky tml. It could enrich the gameplay and lead to more interesting "behind the line" attacks. Their tml are today too weak to make anyone reasonably use the sneaky tml option.
Of course all this requires a wise decision about how to change the tml behavior. This would have to be discussed in further details.