Did you check morale and discipline?
Edit: I thought so. Velites have higher skill, mass, morale (by 3 points, no less), and discipline. Their secondary weapon is technically worse but against infantry still at least as good as the Leves' spear.
Check for yourself:
Velites
Leves
Leves are only better against non-ranged cavalry. Or if you just want to pump out as many javelins as possible.
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