If you had to buy an upgrade in order to make nukes, we could reduce the price of nuke subs. And we could get rid of the whole "Sera battleship nukes cost more because we know Sera players have to make battleships anyway so giving them same-price nukes would be OP compared to what other factions have to pay for separate nuke subs so we will also make Sera battleship nukes a little bigger to make up for the increased price."
This upgrade should be un-cancelable, pausable, it should be started automatically when the unit is created, but start paused. And it should be capable of upgrading while the unit is moving. So every time you make a "nuke sub" or a sera battleship, it always starts with the upgrade paused and you can decide whether to unpause it. There's no reason to allow it to be canceled.
If we're going that route, perhaps T3 subs should only be able to fire tactical missiles when they are surfaced. I like the idea of making it matter whether a sub is surfaced or not.
There other ways we could use upgrades to expand the game:
Upgrade to Ythotha to add a regen field. If they buy that upgrade, when the ythotha dies, the "lightning storm" does no damage at all, but continues to provide a regen field for allied units. So this upgrade would make the ythotha "safe" to send with your army. You would get more use out of them if you had the option to send them with troops without worrying that your ythotha will be sniped down and then your entire army gets fried.
Monkeylords should have a very expensive cloaking upgrade. It should be expensive to make the upgrade and after the upgrade finished it would cost a lot of energy to have the cloaking ability active. But this would make monkeylords more relevant even into the very late game.
Upgrade to t2 pgens to add an armored shell. It would primarily cost mass, not power. It would add a lot of HP (and for Cybrans, add regen rate). When an armored pgen dies, it has a smaller death explosion/blast radius. This would be an alternative way to protect against snipes. It goes against the current meta which is that you want to get T3 pgens and then recycle your T2 pgens to get mass back. Instead you would be spending extra mass to make them safer.