The 8472 are kind of cool, but they are exactly like the Protoss from StarCraft and the Covenant from Halo. And the Protoss came first.
I can't comment on the Protoss since I don't know StarCraft nearly well enough to do so, but saying that 8472 are "
exactly" like the Covenant is not even in the ballpark. I don't even see any real similarities beyond their base concept, i.e. "powerful, xenophobic alien race that wants to destroy us". And the Protoss, 8472, and the Covenant are
hardly the only three examples of that concept.
And 8472 came first, anyway (before the Covenant, that is, not the Protoss).
I dunno - you see one sweet-looking xenophobic planet-destroying race, you've seen 'em all, right? Seemed fine that they'd actually get a dialogue going with them - you can't show a race like that more than a few times and not peel away at least a little of the mystery - hence making them a little less scary each time. Both of the aforementioned races seemed amoral from an outsider's view, but they were a bit more more complex when seen from an insider's point of view.
8472's involvement with the Borg made them more interesting than just another "sweet-looking xenophobic planet-destroying race", at least to me. But I agree that they couldn't be sustained as straight-up enemies forever. Peeling away "a little bit" of the mystery and making them "a little less scary" over time would have been fine. Problem is, they ripped the mystery to shreads and sapped all the scariness away at once with "In the Flesh."
The 8472 thing was just another one of VOY's no-win scenarios: They invented the 8472 for one story and one story alone, Scorpion. They were meant to simply be a plot device to keep the Borg off VOY's back. Problem was, the writers had no intention of keeping them around but needed a quick cheap way of getting rid of them. The result was "In the Flesh". Quite, cheap, no budget-gobbling space battle, and gets them out of the Trekverse.
I don't see it as a no-win scenario. "No-win" implies that it was not of their own making, or in any way their own fault. It was the decision of the writers to introduce 8472 in the first place; if they really were THAT difficult to work with, it's a problem they made for themselves (the writers, that is, not Species 8472.

)
Removing them as a threat force does not require
literally removing them from the Trekverse entirely. It also does not require any budget-gobbling space battles.
I have no problem with doing an 8472 ep that does ultimately dial them back as threats. But they didn't have to just WRECK them. That's my problem with "In the Flesh." One ep is all it takes to comepletely sap them of any punch. The ep didn't have to end on this "We're all friends now. It was just a misunderstanding. Never mind that we are a fundamentally different species from a fundamentally different type of space; we've reachd an accord. Here's a flower." What would have made more sense is for the ep to have made it clear that a full-scale 8472 INVASION is no longer imminent, but that doesn't have to mean that everything is hunky-dory. The 8472 could have decided to reign in their aggression toward our galaxy, but in sort of a "probationary" sense; they're not going fly in with guns blazing for the moment, but that doesn't mean they're completely satisfied that our galaxy still couldn't represent a threat to them later.
It was more along the lines of "Aw crap, the audience liked those Cthulu aliens too much but we invented them for one story and one story alone and then did that story without killing all of them. Also it's too expensive to use them again because of CGI. How do we get rid of them in some low-key, inexpensive, one-episode way?"
You KNOW this for a fact, this bit about the writers having intended from the very beginning to use 8472 ONCE and ONLY ONCE? How?
And maybe I'm way off-base here, but were the 8472 THAT expensive to show on-screen? Significantly more expensive than all those space battles from DS9 season 4-7?
Unless they realised the modified Borg Nanoprobes made THEM the weak ones, and suddenly "the weak will perish" becomes a problem for them.
That's how I saw it.
Where they come from they had no opposition and they were supposedly ripping throught the Borg it tissue paper. So to them, we all were weak.
Creating a weapon that kicked their ass, now made them the weak ones. So they had to alter their plans.
That's an interesting thought, actually. Realizing that any aggressiveness would cost them (which wasn't true before) would give them pause, which could lead them to more closely examine some of the non-Borg residents of our galaxy, which could lead to something
like "In the Flesh," I just think that the way it was presented in the ep, the 8472 "problem" was wrapped up far too neatly and far too quickly.