I like Nuget, but most of the time I think it pollutes the projects too much with lots of unnecessary files. In the end for some projects, I prefer to remove the nuget package and manually manage the dependencies it to avoid the mess.
While some of it could be fixed by package developers, 2 simple things could be done to help with this problem:
1. Have a way to list which files are inside the package in the nuget website and command line. Most package managers for other uses have this and
2. Allow for us to choose which files should be copied to the project. This can be an advanced option, and when you update the package you could be presented with the screen to choose the files again.