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The biggest difference is that the AEC is a weapon that requires a strong mage to even use, and those are few and far between. A regular person can't just pick it up and start killing people with it; they can't power it, making it a big, unwieldy club in the case of the hammer and the cannon. And furthermore, those weapons are thus far only in the control of the Bureau, who can govern their use.
Isis is an unaffiliated possible mage who uses magic to cause physical damage using chemicals. A wild card, who is already instinctively mistrusting of the Bureau. The Bureau, as such, cannot control her like they can with Nanoha and Vita and the others.
So you tell me who they're going to trust more with such weaponry.
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