NuGet scripts to different directory

At the moment, NuGet doesn't support installing packages resources elsewhere than the default location. There's an existing NuGet work item that would cover this feature : #1914 - Allow package resource folders to be configurable.

Not really an 'answer', but worth noting: With the shift of managing front-end libraries to Bower, I don't expect work item #1914 will ever be implemented. I'd highly recommend to look into how you can use the combination of NPM, Bower and Grunt to achieve your custom folder structure.

If you had an early look at VS2015, you'll notice that's the new recommended way for your project set-up and maintenance.

Bower

Dependency management tool used for managing front end components writting in html, css, jss (e.g. Bootstrap, Knockout, Angular, moment, lightboxes, gallery libraries, ...)

NPM

Dependency management tool used for managing node js modules

Grunt

Grunt is a javascript task runner tool. You can do a lot of things using grunt which you had to do manually otherwise: compiling files, linting files, moving files, ...

Difference between above three explained in detail here: Difference between Grunt, NPM and Bower ( package.json vs bower.json )