The players are confused, because the DM is relying on a skill not being present to make the conspiracy understandable?
No, he's relying on the skill being present, and of course (if the DM is sensible) this would only be a critical thing to know in the adventure if the PCs have shown past form for going around making Nature checks.
It would be different if animals were things that adventurers need to prepare for, but they almost always are not, OR the defenses against them are plainly obvious even when not face to face with the animal (giant spiders? Anti venom and some way to escape webbing is basically the most complex thing you can get).
Let's just say you seem to play with very different players to me. In my experience, if players have taken Knowledge Skills *and they want to use them* (which is fairly likely) then they will be wanting to roll all the time in planning and exploration phases and wanting to do something creative with the information they find out.
Like I said - the DM can go out of their way to make the nature skill more powerful, but the same can be said for every skill, so the point is a bit moot.
No, it's the
players that make the skill powerful. The best(?) that the DM can do is obstruct the players in their attempts to do so.
The same logic which says "knowledge nature can be used as insight on animals" says "knowledge arcana can be used as insight on elementals", so again
Yeah, but Nature and Arcana are not Insight (and vice versa), so while sometimes, in a given situation, a PC could get similar information from more than one skill, it isn't the same. For example, if a PC wants to know whether a particular predator is confused by bright lights, Nature will tell her about the species in general, Insight will tell her about the specific animal she has cast
Dancing Lights at. The answer might not always be the same.
Every skill has been broadened, and nature is still applying to some of D&Ds weakest creatures that are also incidentally the least negotiated with.
Well, yes, only a tree-hugging, hippy druid negotiates with plants and animals. But, other PCs variously avoid, capture, harvest, eat, stampede, hunt, sell plants and animals. For a start, not every PC Wizard gets their spell components from "Ye Olde Bargain Magic Emporium".