I'd like to be able to place layers into folders (like photoshop) just to reduce visual clutter, the shy button hides everything and doesn't allow customization and precomping obviously causes issues if you have adjustment, 3D layers etc
As bubgun says, this is a common feature request, but there are some complications and use-case questions that have prevented the AE team from implementing it yet. Talking to your fellow users about it here is useful, but it would also be a good idea to file a formal feature request so Adobe can hear you too. File it here. And make sure you explain with as much detail as possible how you would like it to behave.
As far as precomping goes, a lot of what you have described as issues can be solved with proper use of the collapse transformations switch.
aescripts.com offers a script that "simulates" this workflow, although I've never used it since it seems like whatever time it might save you would be wasted in interacting with a 3rd party interface. I forgot what it's called but it should be pretty easy to find there.
Pre-comps are essentially folders that you use to group layers or change the render order. They are actually very easy to use and manage and edit. Uber-twril - the ability to spin open a nested comp (pre-comp) has been on the feature request list for many many years. Maybe it will come, but for now learning how to efficiently manage a complex project requires you to learn how to use and manage pre-comps and nested comps.
I've used AE and Node Based compositing systems and both have their advantages. Both can get incredibly convoluted very quickly. Both require training and constant practice to use efficiently because visual effects compositing is very complicated.
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