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Easy to play against: Elves and Necropolis. Although, if an Elf uses the right Chaos strategy. And Necropolis is simply weak against it.
Difficult to play against: Academy and Dungeon. Dungeon is just a strong faction! Academy (I haven't played much with them). I think it's because of their magic.
Neutral: Dwarves and Haven... it's just my opinion. IMHO.