Why did everyone bitch about the bossfights so much
Because they sucked in nearly every single way possible.
The areas sucked, they were obvious arenas, disconnected from everything else and not part of wider context (context you could also use).
The fights didn't take into account many of your character development avenues.
The fights started with cringeworthy cutscenes featuring AJ's incompetence and derp, and preventing obvious preparations (when first playing I was carrying a hacked turret around when nearing Barret, because I expected it to become useful - well, it would if I wasn't forced to drop it).
The fights were retarded mechanically, with bosses taking humongous amount of gunfire to take down in stark contrast to all the other enemies who did behave like (sometimes augmented) humans rather than MBTs.
The fights also didn't allow nonlethal which didn't really affected me personally, but it set them apart from everything else even further.
The above points sum why the fights felt completely anti-DX which was grating.
The bosses themselves sucked, because they played no purpose in the story other than giving you a bunch of faces to take out your anger on. They were non-characters and they just as well might have been ordinary specops mooks like all the other without changing single thing about the story.
The only bossfight I almost liked was Yelena as it was somewhat atmospheric (DX1/GiTS style) and the "arena" made most sense to be isolated (ammo and weapons stored there didn't, though).
How bizarre was that final boss fight without Missing Link setting it up?
It was bad even with it.
The entire Hyron project felt like something they threw in just to make antagonist more unambiguously evil to avoid confusing retards and the only thing about it were creepy terminal messages.
It was the strongest one mechanically, though (that's not saying much) including ability to shoot the bitch through glass with laser.