Is it possible to have one scene create another, and have that scene load art from a file?
Say you had a scene that let the user build a tower out of blocks, is Unity capable of letting the user create a new scene, independent of the first, that imports the player’s tower from a file?
Can Unityscript import a 3D object from a file and put it in the scene?
Scenes only exist in the editor, outside the editor, scenes do not exist and can not be created either.
If you want to let the user build something you will likely do so through bringing them into an empty standard building scene and load the level content from some external file / webservice (if it is a webplayer).
Loading models not present in the application isn’t possible without writing an own mesh loader or buying / using one of those available (for obj format)
can you explain mesh loaders? Sorry, by scene I meant application. 
A mesh loader is code you have written thats able to load some external data and make a mesh from it. Unity does not offer any inbuilt way to load meshes that were not in the project at compile time or were in asset bundles or in short: without you writting the code for it or license existing one, a built client can’t load any meshes from the disk etc
You mentioned that there are paid options, can you provide links please? I haven’t been able to find any via google search.
Eric5h5 offers an ObjReader, you can find it on the asset store (in unity window - asset store) by searching for exactly that (its mentioned there as being by Publisher Starscene Software)
Awesome, thanks!