As for the gorilla-banana problem, I would think all objects in a scene would be under the root, with the exception of pieces that make up a thing and rarely separate (wheels on a car, for example).
Additionally, you can throw OOP in that mix as well, because Three.js has it's own whole OOP-style framework, that you're strapping declarative React on top of with this renderer. Reminds me of Jonathan Blow's talk on the end of civilization via endless layers of abstraction[1].
I really think, when it's ready, a Bevy[2]-style system either native or compiled to WASM with WebGPU will be ideal.
And while I'm airing opinions (forgive me), I think writing shaders now is like SQL 30 years ago. Developers left optimizing difficult--according to them--SQL to database administrators by abstracting it away into ORMs. If history is any indicator, I think we'll be having the same arguments on Hacker News 30 years from now about 3D frameworks vs writing shaders directly as we're having now about ORMs vs writing SQL directly.
This provides tons of benefits, so for example you can also decide to iterate over the entites by shader program and gain significant speedups for graphics processing, or maintain components that roughly sort them by their position in world space for physics and culling or lighting, etc.
For a crude analogy, imagine if Document.querySelectorAll() were a zero-cost abstraction, i.e. it ran as fast as iterating over linear memory. In practice this isn't how it turns out with an ECS, but it's much closer and you can get this kind of performance for the "hot path" kind of queries.
To add to the sibling comment, there's another wonderful Rust ECS called shipyard[0] and I helped write a scenegraph for it (which I really need to update, one of these days)[1]
Let's say you're building a game where you want a sphere to stick to whatever player you throw it at. How would you do that with a scene graph/OOP model? It'd be awkward, removing objects from one parent and adding them to another. Even more awkward if it's a complex object and you only want a part of that complex object to stick to the player. ECS + a constraint or physics system does a decent job (not perfect) of handling this in a relatively elegant and performant way.
I've used Three.js enough--built my portfolio[1] out of it, and then switched to Babylon when I realized how little I liked Three.js. For the record, I also dislike Babylon.
could you go more into detail what you mean when you say "anything non trivial"? is there a real example of something that would not be possible to create in, say, threejs?
There's some excellent demos of how this works with this library with a full physics engine. Loads great even on my phone.
If you have a coffee cup on a table in VR, is that coffee cup a child of the table? How do you move the coffee cup off the table and put it onto another table? Is it now a child of that other table? What about the coffee in the cup? Is that a child of the cup? How do you change properties of the coffee without necessarily accessing the table and the cup?
Developers working on 3D systems have developed much better paradigms than the DOM for dealing with this problem. An Entity-Component-System architecture with "constraints" is the current best solution. In that architecture, you would create a coffee cup "entity" with a mesh "component" with another "constraint" component, constraining that coffee cup to the table (or better yet, mass component acted on by a physics system). Then you can simply remove the constraint component when removing the cup from one table, and re-add the constraint component when adding it to the other table.
Overall, I think web developers are in for some intense learning and paradigm shifts if 3D becomes the norm.