The Borg were not the lesser of the two evils, the 8472 were still worse. They were going to commit xenocide, and had the power to do so. The Borg do not have the power to do so, otherwise they'd have assimilated the Galaxy by now. If she'd done nothing, the 8472 aliens would've just killed everyone else once they were finished with the Borg and the means to now kill the 8472 would now be gone so they couldn't make the nanite weapon. The 8472 can make up all the excuses they want, but they were the worse ones who only were forced to the table unwillingly. The Borg are way more stoppable than them. And of course, if Q had popped up after "Scorpion" and said "You save the Universe from total annihilation, kudos." no one would be complaining.
Except in "In The Flesh" Species 8472 claimed they were acting in self defense and were not planning to destroy all other life in the galaxy. There is a serve disconnect between Scorpion and In The Flesh and if the events of In The Flesh are correct, Janeway did something worse then Captain Ransom ever did. So either Species 8472 wasn't interested in killing all other life in the universe, but sent messages saying they were, which would be really stupid, Kes was idiot who misread their messages or Species 8472 were planning on destroying the universe, but were wimps who talked a good game, but when Voyager gave them a bloody nose, they turned into total wimps and changed their story. None of these options reflect well on the writers, two of them make Janeway look really bad and the third one undermines the tension from the Scorpion. Imagine if the Daleks give up on killing all other forms of life, after the Doctor managed to kill a few of them, they would not be very threatening or manage to become the iconic villains they are.
That's basically it. They wanted to wrap up the 8472 thing in a permanent manner, and didn't want to do a big stupid 200 part war story. The Daleks were never stupidly overpowered in the first place, since the Doctor nearly always manages to beat them on his own. They were never introduced as some super-enemy, they became that over decades of stories. You want to create an iconic villain that can be repeatedly used over and over, you don't make them stupidly overpowered to begin with.
1. That is really weak. It turns a scary enemy into total wimps. If they are going to space Nazis, they have to tougher then that. The Nazis did not quit after giving them a bloody nose. 2. That is not made very clear, to the point that I could easily believe the other two theories are just valid. Really Species 8472's story arc was not handled very well and because of that, it is easy to believe Janeway picked the wrong side and Species 8472 were not as bad first appeared. Or they could have not had them appear after Scorpion, if they were going to become total wimps and just flat contradict Scorpion. That was a bad and unneeded conclusion, I rather not have seen ever again then have that wrap up. Besides ongoing story with Species 8472 might have been better then a lot of the bad episodes we got instead, I think I would have preferred that to Unimatrix Zero. The Daleks are still pretty powerful, they did manage to wipe out the time lords in the time war. Really the Daleks were better realized villains, because the writers didn't try to ret con them into something total different by their fourth appearance.
In their second story they had conquered the Earth, ruled it viciously for a decade and burrowed all the way to the centre of the planet to insert a gyroscope and turn our homeworld into a mobile battlestation. "Meh." The Daleks spent thousands of years in a stalemate looking for the perfectly logical opening move against the Movellian fleet. Seriously, battle computer vs battle computer out predicting each others gambits unwilling to commit resources to a shitty first move. You have to admit that that is similar to running away at first blood.
Voyager didn't have the cannon fodder needed to maintain an enemy like that. Doesn't help that the Borg (the other half of the conflict) are too boring to use as an enemy themselves. That's too open-ended. They wanted them gone in a final manner, and didn't want to tell a big stupid 200 part story to do so. You can't telling ongoing stories with an enemy that stupidly overpowered, you tell ongoing stories about enemies that are at your own power level or lower. The Daleks were just a normal enemy of the Doctors for like 20 years before they started treating them like some big threat to the Time Lords. For all their early appearances, they were NOT some big threat the Doctor felt he should be afraid of, they were just some normal enemy. Doctor Who's time-travel story aspect meant they could also tell stories of the Daleks' at various points of their strength and not have to bother with a linear story. For crying out loud, in the 80s (even after the Daleks were some big threat) we saw them getting killed by a teenager with a baseball bat.
To be fair, Ace's bat had been tinkered with to make it more destructive. I forget the specific details. It kind of annoys me how the Daleks got such a huge boost in their threat level. Since they're the most popular monster in the series, they apparently have to be the most dangerous, even if it goes against what was going on in the original series. It would've been so much more interesting if the Time War had been a civil war, being fought by Gallifrey against itself from two different points in time. But as to Voyager, one of the things I really like about Voyager is how they are on their own, there's no chance for backup in a strange quadrant. Everything is harder, the stakes are higher, and the choices Janeway had to make were harder, and the writers didn't go easy on her, she frequently had to make really difficult moral decisions, like with Tuvix. At times there was no good choice, just a choice between two bad options. I was disappointed that the surviving Equinox crew never got used again. Seems like a wasted opprotunity to me.
The Hand a Omega, a stellar manipulator, that casket the first Doctor Burried in 1963 and then 7 dug it up to destroy Skaro... It had the AI of a clever Dog obeying instructions to follow, upgrade or exterminate. I don't think that it's a single serving weapon of mass destruction. 7 could have exploded a great number of stars. In a recent audio story 7 said that he's seen the future, and his next incarnation is such a nancy pants wofter boy milk sop that there is no way that junior can survive in the universe as it stands until after Seven has finished babyproofing it for the 8th Doctor. Sylvestor McCoy has taken this to hearts with an evil glint in his eye and repeated the sentiment verbatim in a behind the scenes post show interview as the gods own blessed incontrovertable truth which he beleives in.
..but this is Star Trek, where the Captains are never wrong and every enemy is just misunderstood and eventually an ally. Star Trek is about making friends.