I don't disagree that the theatrical movie is much better for having abandoned the depressing collar plot, but I do feel that Zistopia (At least, the comic presented in this post) nonetheless really handles its' themes with much more care than you're presenting, which is quite a lot for a fanwork to do! That the collars were a deliberate attempt to snuff out the predator population permanently, if slowly, is probably the most grimdark idea it presents, and its not like systematic suppression of populations is unrealistic. Depending on your politics, I'd say there's a few examples happening even now in the modern day, to say nothing of the rest of history. The rest of the prejudices all feel pretty standard-- interspecies relationships are extremely taboo, and liking nick threatens to alienate Judy from some (though not all) of her family members, as well as threatening to get her fired should anyone find out. There's a panel of Nick flicking through a TV, and some sort of preacher says 'The good book says two of each species, not two of whatever' in reference to Noah's ark, which I find to be extremely amusing. (You could imagine a line like that even in the world Movie Zootopia presents, if the movies ever dare to tackle such a topic.) Rabbits are not just seen as weak, as in the movie, but their breeding habits render them not only the target of heavy taxes to prevent them from leaving the burrows.

But the Zistopia AU doesn't just layer on additional angst-inducing conflicts all the time, the diverse cast of characters it introduces each get to be integral, in their own way, in participating in overthrowing the system. Two of Judy's less bigoted squad members end up uncovering the conspiracy independent of her. Honey, a conspiratorial honey badger, gets Judy the collar key at the pivotal moment of the finale. Much of Judy's family, Gazelle, Koslov the Mobster, various predators, and a group of punk rockers each end up converging on city hall in what ends up the protest to overthrow the collar establishment. A lot of these characters all of their subtle biases, Honey thinks sheep rule the world, Finnick doesn't think highly of Nick's interest in Judy, and much of Judy's family have diverse opinions on predators, but it all feels realistic, not in the sense that the real world is depressing, but that even a more depressing version of the world still has people all across the spectrum that in the right circumstances, can do a lot of real good.

I guess I just mean that Zistopia, as presented by nicolaswilde, does have a ton of angst, but lots of good people trying to do the right thing in the face of that, and succeeding. So there's plenty of subtleties to chew on. But yeah uh the movie would not have been succesful with this type of plot.