I assume if the player is hit with an EMP while wearing PA, that the PA's defence effects will disable for the period of the EMP so that you lose a lot of the Defense Rating for a period while still being slowed down with the power armour. Possibly disabling the ability to change or unequip your Power Armour for the period of the EMP blast duration effects too.
The fusion core powered Power Armour is a fantastic idea and I look forward to playing with it. Although I'm sure I will be wearing the Merc Grunt Outfit or something for the first 20 play hours until I level up I plan to use unarmed because when you take unarmed perks, it does a lot of damage especially if you use Spiked Knuckles which do 1 punch every second, so you deal damage rapidly. I think Merc Grunt Outfit/Leather Armour etc is more effective than PA for this type of battle, so that you can move quickly and dance like a bee around your opponent to dodge their melee attacks while dealing your own damage. Although if it was a Super Mutant with a SuperSledge, I would equip the PA or switch to Energy Weapons.