I had an idea regarding the Necropolis faction: in all games, Necromancers are debuffers. Maybe we could allow each unit to apply various curses. For example, the first-tier units could apply a weak debuff, while dragons or other high-tier units could apply Berserk or Confusion at the expert level.
Added 31 seconds later
By the way, you didn't respond about the Mountain faction. Is the idea of replacing the class ability "Absolute Protection" with "Terrifying Presence" acceptable?