more point for point
You're doing that thing where you rail against your nebulous perception of fandom, so I'll just stick to my own opinion. My biggest problem with the handling of 8472 was Voyager coming up with the weapon that beats them. It made the borg look rather rubbish. 8472 ships blow borg apart with ease whilst Voyager survives a round of combat then returns fire and blows 8472 ships apart. If Voyager had stumbled across some ancient alien tech to enable their anti-8472 superweapon that would have been less annoying, albeit still a bit contrived.
honestly if I was writing such a story I'd just have 8472 and the Borg blasting seven hells out of each other, to some sort of stalemate or narrow victory. And Voyager simple doing its best to evade and survive.
The wider problem with the Borg was, we ended up just not that scared of them. Maybe because they were used too much, and thwarted too often. It was a serious case of what TV Tropes calls Villain Decay. (Who has a similar problem with Daleks) In which case, yeah, Voyager was at a disadvantage simply by being later to the party. Although more inventive writing could have helped.
We already knew there were entities out there that could overpower the Borg. We met a particularly godlike one in the TNG pilot! But a story like that has to be handled carefully in case it contributes to the Villain Decay. Maybe if the Borg got totally beaten, and then 8472 took over their space, that would be more interesting. But the Borg hung around instead, going from a top level terror to bumbling cyberzombies.