My suggestion would be quite simple - there should be more caves in DF, and those should be quite attractive for those who wish to avoid prying eyes. As such, necromancers should use them to hide from the world. I remember how fun it was when, iirc, in Oblivion the necromancers were hiding in caves with all their books and equipment, to practice dark magic in seclusion. I would love to see something like that in DF. In an advanced civ which has settled vast lands, and possesses a large army, a necromancer tower seems odd - they should have tried to destroy it somehow, but making necromancers hiding in the shadows, kidnapping innocents and taking them to their caves to conduct their experiments - that seems much more immersive.
It would also be fun to make learning necromancy quite hard, having to learn different skills one by one - from the very basics of life and death, followed by simple spells, raising dead animals, then raising dead sentients, to summoning dark beings, which if not properly controlled, could kill you as well. To learn many things you could need sentient beings, which can complicate it a bit, to other you need corpses - that could complicate things too.
But basically - I love the idea of more secluded necromancers, unless of course the civ accepts dark wizardry, and for necromancers to be hunted by inquisition-like forces, and tortured upon capture. This would make being a necromancer much more challenging and FUN - you can potentially get great powers, but you may well die in the process.
Some examples of FUN for necromancers:
- From simple things such as having to practice dark wizardry on captured sentients - kidnapping them might not work at all, and you could be killed or captured. Also, they might escape and inform soldiers where your hideout is.
- To do wizardry you have to brew a lot of potions - those can explode in your face if not prepared correctly.
- You might mix words from an ancient language and screw up an ancient ritual - with many FUN outcomes - such as turning yourself into lice, a werebeast, turning your hands into hoofs, or disappearing in a pink cloud.
- And of course, you could summon powerful creatures that will not only kill you, but burn whole towns and fortresses as well.
To conclude - being a dark wizard could be a lot of fun.