Just a more cohesive undead army with a more interesting backstory and very dangerous units.
You should pickup Disciples 2 if you get the chance. It's a classic turn-based strategy game. Easily worth $20 on steam for the gold edition (which I think is $15 anyways). Disciples 3: Renaissance I can't recommend as much. It tried to be Heroes and was not very successful. Disciples 3: Resurrection (the expansion) was much more successful.
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The giant has awakened
You drink my blood and drown
Wrath and raving I will not stop
You'll never take me down
Actually Disciples' Undead Hordes are composed of the same creatures that the HoMM Necropolis has but they are just made more interesting, with more individuality - which is not surprising because in Heroes you lead armies while in Disciples you lead squads.