I have no idea how tough PULSE Magnezone was supposed to be. I set up Swords Dance on ZEL's last Pokemon. I 2-shotted it once it flinched from a Swords Dance-boosted Waterfall. Not that I'll complain ^^
Honestly story-wise I wouldn't expect it to be particularly tough to beat. Like Breezie said, it's the one PULSE mon that wasn't actually created with a purpose in mind. All others were made to suit a specific task they'd fulfill, but this fella was just a test. With unforseen consequences.