Yes having one area of the UI split into boxes corresponding to layers, with a dot in a box if the layer has something in it and the box colored differently if it was selected was not intuitive at all, I could scarcely understand it’s levels of complexity.
I could access my layers without obstructing my view of the whole scenes contents - which I could set to show only the current layer. Now find myself constantly minimizing and maximizing ‘collections’ with seemingly (correct me if I am wrong) no way to only show the layer, or collection, I am working on? Yes I suppose it is more intuitive if you just remove features.
Remember when you could just select an object, press ‘M’ and ‘2’ and it was moved into layer two? Hideous wasn’t it, not remotely intuitive. M for what, move? 2 for what, layer two? I could never remember it.
I much prefer having to create new layers if I need them instead of them already being there, brilliant change. I suppose you have to create them now, because if they already existed they’d clog up the scene tree - which they never did before.
I have since learnt to fix it - when you import a 2.79 file all objects in other layers have ‘visibility in viewports’ disabled. How exactly was I supposed to figure this out? The eye shaped visibility marker on the right, which usually goes from full to empty, e.g. visible hidden, was in the visible shape but greyed out.
How that is intuitive is beyond me. The fact that when I googled it there are multiple youtube videos explaining it would suggest that indeed I am correct - it is not remotely intuitive.