for complex stuff, node is the only way.

afterfx is the king of layers, and that gets impenetrable pretty quick.

The best way to deal with the spaghetti is to group and route. In Nuke, you can group a bunch of nodes into lump with defined input/outputs. This means that you can hide the complexity underneath and limit the amount of "wire spread"

Node based systems are really good for hooking things up and testing/altering. It also quickly, clearly and obviously shows data flow.

Not all node displays are created equal. Anything that has bendy lines is a non starter (there is a reason Printed Circuit Boards rarely use curvy lines) Anything that doesn't have a group & hide function is also doomed. Its like having a programming language that doesn't have a functions, only goto.