Yes, I agree with @carolhmj , hard to be sure with just the information above.
The point is (if I understand correctly) your app for edit is sketch, next you import it in blender and finally you make an export to either three.js or bjs. The numbers you have here make me think that eventually the interpretation of the imported format is different. May be your faces are exported as triangles for BJS and quadrangles for three.js? May be vertices are converted to faces for some unknown reason (but then, I believe the numbers should be higher). May be only some of your meshes are not interpreted correctly on import… Again, we would really need to have the model for any chance to eventually debug this.
By any means, as stated by @Null, the 25 lights!!! are clearly not going to help getting reasonable FPS. Not to mention that these lights will likely not work with materials/shadows.
I don’t think the materials (even with a count of 90) are the biggest issue (although it has an impact on performance for sure). But then, finally, the 3067 meshes in a single scene also seems a bit above reasonable. I wonder what these are?
Edit: Just a thought. May be you could give a try at this (use gltfpack as per post from @bghgary )