weapons of mass destruction
I'd say in the game you tend to have relatively few fleets and those are pretty big. maybe an occasional smaller fleetlet to protect a cluster of planets, some few times for pronged attacks, but more often than not you're better off keeping your ships together. but that forces all players to equally have main fleet, which I think just does not fit too much to a 4x game (ok, RT4X). so I though of a few sort of soft ways to put a price tag to a big fleet (other than it not being at multiple places at the same time, which is a moot point if all players deal with big fleets as you will hardly kill a fleet 3 times your size without massive defense, brilliant tactics and slip ups from the opposition):
one could be an explosives-laden capital ship that explodes with vast force in the enemy ranks. think of freespace 2, meson bomb carrying orions. in short, you pay as you would for a normal capship, also the slot, and get a tough ship though with no weapons or abilities. except for a weaker version of argonevs big red button. maybe something in the range of 1000 dmg in a big enough radius to encompass completely a large fleet.
a second could be something like a black hole generator that damages ships in the area. has to be channeled (and can thus be interrupted), takes, say 1% health or shield per second or if that is not possible something between 5 and 10 of either. could be an expensive cruiser class ship. important: effects do not stack. you could use multiple of those things to cover the entire enemy fleet, but any ship can only be damaged by one black hole at a time.
the problem I'd see with both ideas is that it makes them prime target and the very large fleets they are designed to counter would take them down pretty fast. though on the other hand, if you made the range large enough, such a fleet would be highly cautious to engage it and try to take these fleet killers down remotely, by fighers for example.
on the whole I think these are sound suggestions as they are potentially very powerful weapons, but have weaknesses and can be countered. the missile would to get close enough to detonate which would be tricky if the enemy directs fire to it. the cruisers attack can be interrupted and does not stack. both abilities should really affect you and allies as much as the enemy as we are talking about wmds. so, yeah, some sort of incorporation of concepts of collateral dmg found in other 4X games, which would benefit the game imo.