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If some form of mothballing was available, many of those challenges and decisions would not exist. I could have created a mothball fleet for most of the battleships and carriers and spent the 'fleet maintenance and refit' resources on improving my economy, or building additional commercial vessels, or building 2-3x more ships in storage than I would have had otherwise. My Gallicite shortage would very likely not have happened, along with all the associated consequences, and my strategic imbalance would be solved relatively easily. I would not fear a major threat with my large mothball fleet available when needed, so creating a large active military available to respond to threats, with all the planning that entails, would not be needed.
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You say that as if mothballing could not possibly take a form that would not obviate those challenges.
If mothballing saves you 100% of the upkeep cost and if reactivation requires only a strategically trivial amount of time, then yes, mothballing does not represent an interesting decision.
But what if mothballing (and reactivating) takes a lot of time and resources?
In particular, what if mothballing and reactivating both require a shipyard?
What if the slipway remains in use while the ship is mothballed, until the ship is reactivated?
What if each process takes twice as long as building the ship from scratch?
What if each process requires Gallicite equal to the BP of the ship?
Under those requirements, "building for mothball" would hardly be an attractive way of establishing strategic long-term security.
Instead, mothballing a portion of an existing fleet would be an option worth considering after using a very large fleet to secure victory in a major war and no longer facing extensive near-or-midterm threats.
Mothballing will also limit strategic choices in fleet design. If you want to create a mothball fleet that can be reactivated years later and still be effective, you would design the ships on that basis. Therefore, you would build carriers and missile combatants, because those can be made much more effective by adding modern fighters and ordnance. It would not make strategic sense to build beam ships that would be completely outclassed without a major refit that would likely cost the same as a new ship anyway. So mothballing will drive you down specific research and fleet doctrine routes.
The long-term design viability of missile ships and carriers vs beam ships is already a strategic consideration.
But the longer a given game goes on, the longer the time gap between significant tech upgrades.
As that time gap increases, the strategic relevance of long-term viability concerns for different ship types decreases.
Mothballing, if expensive, won't significantly change that dynamic.
In the early game, mothballing might be a more attractive option for some ship types than others.
But if mothballing is expensive up front (with, say, a breakeven time in the neighborhood of five years vs constant ship maintenance) it won't be an attractive option in the early game for any ship type.
Once you've climbed up the tech curve a little ways, the decades-long gaps between tech upgrades makes economics the major factor in the mothballing decision. Ship-type longevity won't matter as much.
Even if we had mothballing, finding the right balance is extremely difficult. It has to be a decision that can turn out to be incorrect in certain situations. That 'situation' cannot be simply 'what if aliens attack Earth at short notice', because is it very unlikely an attack of sufficient force to overwhelm reasonable defences would happen without significant warning. No one is going to mothball everything. In economic terms, it's also difficult to create an economic or time-based penalty that is sufficient to make mothballing a real decision without also making it more expensive than simply pre-stockpiling components and building new ships when needed.
In summary, while mothballing does have some mechanics issues, it is really a 'removing challenges and limiting choices' problem.
It's hard to argue with you here.
Stockpiling components (via scrapping or via building new) can be seen as providing, at least partially, the same functionality as mothballing.
You get a shortened lead time for creation of a future fleet in exchange for some build cost now and no upkeep cost.
Maybe we just haven't formulated a complete picture of what a "good" implementation of mothballing might look like.
What if we think of stockpiling as the poor man's mothballing?
That implies a version of mothballing that is "better" than stockpiling components, but is harder/more expensive to achieve.
Perhaps it requires some tech or infrastructure investment and some ongoing costs.
But what could it provide in return?
It seems like it can only reduce up front costs or reduce the lead time for ships becoming available.
I don't know, maybe there's some other strategic or logistical flexibility that mothballing could provide to differentiate it from component stockpiling, but I'm out of brain for today.