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Here is how I understand the theoretical purpose of ballistas and scorpions:
Ballista: Good all-around siege weapon. Decent at killing units and decent at damaging walls. Catapults/Onagers are better at taking walls, but have less ammo/accuracy and therefore not as good at killing troops.
Scorpion: Siege weapon designed specifically for taking out units. Low damage / incapable of damaging walls+gates but has more ammo and faster rate of fire than other siege weapons. The unit-killing siege weapon.
Theoretically, scorpions should be the best of the siege weapons at taking out units...and yet this is clearly not the case in actual gameplay. In my experience with both Rome and Egypt, ballistas consistently do better than scorpions (in terms of kills) and have the additional advantage of damaging walls. I have tested this several times, using up full ammunition for both the scorpion and ballista. The ballista has had more kills in every single test (almost always by a significant amount). So now, I don't bother with scorpions at all, just ballistas.
Has anyone had a different experience? Do you ever choose scorpions over ballistas for any practical reason? Seems to me that scorpions need a bit of a buff against units, or ballistas need a bit of a nerf. I realize that scorpions do cost a little bit less, and I am taking that into account already for my judgement.