Honestly I feel like the main issues are:
World generation. Necromancers have a tendency to wipe worlds clean of all civilization, meaning that a person can get very, VERY upset running world gen after world gen only to have it incinerated by necromancers. They are far too good at conquering the world and that needs to change, it’s one thing to lose a world to a crash and another to lose one to crazy necros.
Adventurer: Intelligent Undead. They are insanely OP, with game-breaking abilities like paralysis, blood syndromes, icicles, a lot of other things etc etc. While this itself would be somewhat acceptable if they were rare and far between, the rate at which necromancer influence tends to spread in normal worlds(especially if they have begun conquering other sites), it means that sooner or later you will accidentally stumble upon one of these monsters, and never live to tell the tale. That also has to be fixed.
Fortress mode: Undead Sieges. They can come when your fortress is still young, spelling death to all but the most paranoid(like me) or prepared. They can also come in large numbers and with necromancer experiments(even experiment corpses, oh god), means that undead sieges are pretty hardcore. Then again, their most broken feature is the ability to trim the young sapling that is your fortress, as any fortress with a semi-decent trap hall and spike hallway should be able to cleanse an undead siege. These may be the least broken of all necromantic abilities.
I think the issue with necros is that they grow too strong, too fast. Basically all other !!FUN!! Producers are locked behind some sort of requirement, or need you to personally activate then yourself. Goblin Sieges? Pop requirement+proximity to goblins. The latter is a personal choice. Forgotten Beasts/megabeasts as a whole? Locked, behind a wealth/population requirement. The circus? You have to find AND break the candy YOURSELF. That’s on you, not the game, for digging too deep. Werebeasts(prominent FUN)? Also locked behind requirements, allowing you to take the appropriate actions to keep your dwarves away from their infections bite. Vampires? Their not actually that bad of a threat. Unless they get your important talent first, you can quickly find and isolate them with brute forcing and checking, neutralizing their threat. But necromancers? It’s like going to the starter area and accidentally falling into the secret boss’ lair...and he is level 100.