Optimally, the game should be able to adapt to whatever magic/technology/mechanics are made, and find its own ”balance” that way. This can be done by actors simulating a few strategies and using the one that works best. This mirrors the real world in that major advancements can be done, but eventually are counteracted. Sometimes, the best strategy may very well be to just adapt that advancement in return. Toady has talked about this (in one of the DF talks, I believe). Something like ”magic worlds are inherently imbalanced, but as long as both sides have the magic it should be fine”.
The problem with necromancers, is that using necromancy gives a clear military advantage, but both sides can’t have necromantic powers. The ”good guys” can’t get necromancy as that would turn it into a crapsack world nonetheless, which shouldn’t always happen, and current necromancers have no reasons to turn against each other, being seemingly driven only by a hatred for the living rather than having a wish for world domination. The living also can’t rise up once necromancers have won. The consequence of this is that all worlds with necromancers will sooner or later fall to the armies of undead, and then become stale, the only balance met is that of stagnation.
So how do you solve this?
You could nerf the necromancers, but then that only decreases the likelyhood that they will achieve world domination. It will still happen in older worlds, as they will have more chances during worldgen in those, just as the chance of getting a Nat 20 is higher the more times you roll a die, even if you switch from a D20 to a D100. Nerfing them too much also removes them as a threat for the player to deal with which would be a shame.
Alternatively, you could allow the world to return to ”normal” by having the necromancers and their underlings fight internally. Perhaps the necromancers really want world dominion? Then you could have late-game necromancer entities replacing the mortal ones. The undead lieutenants may also want some share of the power, or maybe the technically mortal experiment populations could rise up against their overlords, wanting to reestablish the old world. You could even go as far as having some natural counter against necromancers, like divine summoning of new populations of dead races to fight back, or anti-necromancers. But these counters must act after the necromancer apocalypse, and be able to arise spontaneously, otherwise the main problem of necromancer stagnation will not have been dealt with.