Fleet cap on systems would be awkward and super un fun. See my above suggestion for defensive systems that cripple larger numbers of enemy fleets, that's a counter that can be as hard or soft as needed and adjusted as needed.
I agree, I don't particularly like any version of fleet/system caps. (From my earlier post: "People do float the idea of putting a fleet cap on systems. I tend to think that wouldn't work..." Emphasis added.)
Re: defenses that scale with the number of ships/fleets, that might work. @Pancakelord noted the same idea above, but with more detail.
Personally I don't tend to prefer that kind of solution for two reasons. First, it doesn't change the basic incentives of warfare. We'd still have the same problem we do right now, that the only way to decide a war is by destroying the enemy fleet. Second, relatedly, it only deals with system defenses. It doesn't change the fact that the only way to fight a doomstack that doesn't attack your fortresses is with another doomstack.
Not to say that you're wrong, certainly. I just would prefer a solution that comes at this from the strategic level. The tactical approach is to say "if they have a doomstack, how do I win the fight?" I think it would be better to say "if they have a doomstack, how do I win the war?"
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