@ftxcommando
A personal anecdote, I just won a game of Dual Gap thanks to my nuke subs (and I commonly build them on any map with a lot of water). As to the ideas presented here I actually like all of them, haha!-- Billy nuke and TMD rebalance, or slightly cheaper normal nukes, or even the upgrades idea @veteranashe presented.
Nuke Sub Rework
Found this thread through search because I was curious what else had been said on the topic.
What if strat subs had some version of the above-mentioned tactical nuke ability, but could also load strategic nukes from SML(!) that were carried to them by transports(!!)?
Non factor. It's a transportable luggage unit with a script to add and remove ammo when added to storage. Payload and range can be whatever you want on either launch platform. Could even make the warheads able to self-destruct and transportable by ACU/SACU/engineer for a bit of ground-and-pound.
I felt that an idea to rework nuke subs fit perfectly in in thread titled "Nuke Sub Rework".