Biggest pain in the ass? Hmmm, probably the Neochu fights, without using the Death trick on them. Other than them, mission 62 with the two Ratjavikias is probably the hardest fight in the whole game, being that it can't be done with any cheap method.
Story bosses aren't hard per se, with the exception of maybe Brynhildr (I got her only at the last 5 seconds of Doom) and probably Cid (I had a bad Paradigm preparation going to the fight on the first time). Other than them, bosses were relatively easy.
Current PC Build
CPU - i7 8700K 3.7 GHz (4.7 GHz turbo) 6 cores OC'd to 5.2 GHz with Watercooling (Hydro Series H110i) | MB - Gigabyte Z370 HD3P ATX | Gigabyte GTX 1080ti Gaming OC BLACK 11G (1657 MHz Boost Core / 11010 MHz Memory) | RAM - Corsair DIMM 32GB DDR4, 2400 MHz | PSU - Corsair CX650M (80+ Bronze) 650W | Audio - Asus Essence STX II 7.1 | Monitor - Samsung U28E590D 4K UHD, Freesync, 1 ms, 60 Hz, 28"
