Ermh, did you not notice the "self-guided bombs" the machines had? They first used them in Reloaded, remember?
Also, we have computers now that are EMP Shielded. You'd think the machines would have come far enough by then to be fully EMP shielded (especially considering their progression in other fields).
Oooh, ooh, don't forget the fact that Neo somehow regained his.. oh, sorry. Spoiler.
Anyway, yeah, there are many stupid things in the Matrix, but it IS a SciFantasy movie, after all.
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