It would also allow for more varied battle roster in general, not just historic-wise.
Think of how many times you've been 'build as many X as possible, with the occasional Y in support.' If you had a limited pool of each unit, that would result in relative force-concentration across a front - Do I place My ISD2 here, or my ISD1? Or could I just hold with my Victory-1 and two Carracks?
Also, don't worry too much about balance wise when you do this. You should be able to rough-calc it initially - An MC80 is equal to a ISD1, etc - as it's what you do with regular pricing and pop cap. Hell, just doing the usual credit & pop limit, but with a limit to particular ships numbers, would work.
With Steam, you could easily update the battle rosters with updates.
Obviously not something for 2.2, but maybe 2.3/4.
Well, the original suggestion was choosing different historical fleets, which while that works for the battle that fleet was from vs the other fleet in the battle, where you start with everything vs everything, no production, it doesn't work if you had one player pick, say, small task force A from battle B against giant fleet X from battle Y, that's what I mean by balance being an issue here. IT would have to be left as a specific Total War-esque historical battle, which would be a separate thing, and that's something we'd like to do in the future.
As for your suggestion, unless I'm misunderstanding, that would just boil down to being a regular skirmishw here every unit had limits. There's a few problems with that- for one, it would mean that for whatever different limit you want, you'd need a new set of variants, on a new set of maps. The game would have to treat them as entirely different units, and that's how you start massively bumping up lag and loading times throughout the mod. Moreover, if you're producing these ships and you have an overall limit on everything, you'd get to the point where, after the main abttle, neither side may have anything left that they can build, and you just end up with fighters vs fighters. Ultimately, if the goal is to prevent spamming one unit, the better alternative is to wqork towards trying to get balance to a place where people
want to build more of a variety of units, as opposed to putting a unit limit on skirmish for everything.