What type of files should I use for babylon? Preferably with everything in 1 file(mesh, textures, animation) to make things simple.
Can I use like a generic animation, for example, in a skeleton and apply the animation to any character with the same animation? Or should it be saved for every 3D model file?
If you want everything in the same file you can use .glb files, which are the binary version of the gltf files.
.babylon format, which are the native file format, can also hold the data but may not be supported on your DCC tool (if using one).
You can have a single skeleton with animations and apply this skeleton to multiple different meshes. Look for the animation section in the Babylon doc site.