I can more than understand that; no fight should be taking more than 20mins at most so I'll definitely review him. But his defences are supposed to fall if his Armour is destroyed beforehand (the lower target, called Jamar Armour or Proud Armor). Was this part of the boss killed and damage output on the torso remained more or less the same? If that's the case then it's an AI bug. I can shrink the statuses too; defence-wise, try Protect Vests to reduce the damage from Shoot attacks by 1/2; should work against Mako Cannon, any machine gun attacks, and generally anything that fires a beam/projectile.
IIRC, his defenses didn't drop for me either. I dealt with it and just beat him anyway, but killing Jamar Armour didn't change anything for me. I could go back and try again, I think I kept a save file not far from the boss.
By the way, now that I think about it, I recall a problem with a random encounter in the same area, with the Grosspanzer enemy. Killing the two turrets and the main unit didn't make the last part vulnerable to attacks. I tried everything from Dispel to Ailments (I even waited a few minutes just to see if it was just a timed condition), but he just kept attacking without taking any damage.
EDIT : I just went and checked, and killing Proud Armour indeed does nothing.
By the way, I think the boss was fine, especially compared to his original appareance where it is a pushover. Mako Cannon is really dangerous, but it is also very slow to start, leaving enough time to Heal and maybe Defend. As for his other attacks, I feel like his damage isn't that dangerous if you manage to keep Wall up. And Aerith is very nice for this battle, since Planet Protector takes care of any problem.