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And most importantly, the balance when a Necromancer can permanently destroy an opponent's city is completely unclear to me.
If a Necromancer captures your city, you can basically say "good game, well played" 100% of the time, at least in duels. And even a converted city isn't that useful to the Necromancer himself, especially at first; it still needs to be rebuilt. And on maps with 3+ players, there are heroes who are many times more useful.
There's a skill there that seems to be designed for the Necromancer: "Lord of the Dead." The only thing is, I think they forgot to rework it after the changes to the released version of Heroes 5 - instead of being useless, it should give some amount of dark energy instead of the current 5%.
I hope they fix this in the future.
This skill is useless, yes, but the question is, how is it even related to Mentorship? No one is forcing you to level it up. Unless you're leveling up Spell Power, but Spell Power beats itself in one out of a hundred situations, figuratively speaking, considering that you managed to catch it. And in general, Necromancers are rushers, and leveling up two schools of magic, neglecting defense or logistics, well, I don't know, it's not always possible to cast everything you need from one leveled-up school, let alone two.