I think nothing can beat the native JSON format due its ease to create, maintain and manipulate the file.
Yes, file size can increase a bit, but, gzip compression is always recommended anyways.
The biggest benefit is the material assignment. I don’t ever need to worry about material hacking within the app itself to make it look as I wanted. The modelers always create the models as close to what it should look like with whatever tools they need. But when it comes to replicating the same material effect with files other than JSON, you alway end up tweaking the material properties within you application.
It is always great to have tools like threejs editor. So, wherever there’s a 3d asset created, I recommend to use editor for material and texture creation. There’s a lot to be improved in editor, but hey, you can always help the community by creating you own features and releasing it as PR or keep it to you as per your requirement.
Open for feedback on my point of view.