I think it'd be nice if we started using the composer autoloader for dependencies like apps instead of moving everything around and symlinking. If we could make Anahita's autoloader compatible (I think it is for the most part), that should be pretty easy to do.
Why would the file paths need to be translated? The point of the autoloader is to find where the files are located automatically and include them, right? The only issue I'd see is with template files cause those aren't classes, but we'd just have to extend the template path.