Some way to prevent the huge fleets from having runaway power and being overwhelming.
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Splash Damage weapons and other patterned multi-ship damage.
A way to vary to-hit chance depending on recent combat events. (eg: The "firing more shots into the big cloud of smoke" effect seen in action movies
To-hit chance could drop by 1% for every 10 damage inflicted on a particular ship during a single combat round)
With those kind of settings, a huge fleet couldn't inflict more than about 1000 damage to any particular single ship in one turn.
All optional, but I think the underdogs could use some help