I think the answer you're looking for here is : needed a cool villain, tossed events from "In the Flesh" right out the proverbial airlock.
That is the best thing that could happen to Species 8472 if that episode was nullified.
I mean it was a neat Trek Episode but for Voyager it destroyed the species as an enemy.
Same thing with the Hirogen, although they did get a little more screentime but if you pay attention you will see how fast they become an unimpressive small, diplomacy talking species that makes peace for Holodeck Technology instead of hunting you down and grabbing 7of9 on the neck and holding her into the air without braking a sweat.
Those 2 were probably the coolest races Voyager ever came up with and they ruined them by making peace way to fast.
And all that was left for "Endgame" were to destroy the Borg. (at least as far as you can destroy them in one episode with superweapons etc.)
If you think about it they couldn't have done anything else because the Borg Colelctive was the only thing left standing.
But then the complete Episode should be ignored including the shapeshifting abilities. (that was more the Dominion / Founder way)... 8472 comes with massive fleets invading your Space shooting your planets.
You know, the fact that humans are 'friendly' and peace-loving would be taken by a lot of cultures as good reason to go conquer them. Especially if they can shapeshift and create a kind of 'They Live' situation in which they control the entire galaxy without having to have very much armed conflict or destruction to do it.
This is why we have standing armies. And why starships are heavily armed.