Scenes
Scenes are the basis for composition in the engine’s editor, so if a project is particularly editor-focused, you may want to create new types of nodes, plugins for the editor, or new resource types that can be edited.
The biggest advantage of using a scene tree, is that the extensive Godot eco-system is primarily designed to be interoperable with nodes structured within the scene tree. The editor also supports inspecting scenes at runtime, which can be useful for debugging projects.
The scene tree is well suited for pre-designed spaces and environments, and/or for artists and designers to work within. If you are expecting to design puzzles, levels, tell stories, or create an art-piece, using the scene tree will be effective as you can design all of the visual elements within the editor and leave any behavioral logic to be implemented in code.
If, instead, you are building projects with more dynamic environments, ie. creative editors, procedural-generation and/or large scale evolving worlds. The overhead and workflow of using the scene tree may be more of a hindrance than a help. In these cases, you may want to consider using a more code-centric approach, such as a Canvas-based approach or the lower-level Rendering Server or Rendering Device APIs.