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It would be possible to create ballistae with race-specific abilities. Or, instead of simply increasing attack power (which would require building a special structure), they could have alternative upgrades, for example: for demons, it could improve or add a fire ball ability; for Haven, it could add a stunning effect (the unit loses initiative for one turn, reducing it by 5); for Necropolis, it could reduce the attack power of the target by 1 with each shot, but the unit's attack power would always remain at a minimum of 1; for Academy, after each shot, the ballista would increase the mage's magic damage by 2; for Dungeon, it could reduce the target's defense by 1; for Sylvan, it could entangle the target with roots for 1 turn.
Plus, with each skill upgrade, the effectiveness of the ballista and its abilities would also improve.
If there are new machines, then new heroes and new skills and abilities will have to be created.