I know what you mean twmulloy, it seems inconsistent to have 'view' related information in different places. However, consider that the JS and CSS files are resources that support the views, rather than parts of the view themselves.
That said, you can achieve what you want in a number of ways. One might be to write a controller that accepts requests for your JS/CSS assets and outputs a header and data from the relevant place (a view file, the database, anywhere in fact). However, this is inefficienty compared to just accepting the 'untidiness' of popping the files in a subfolder of the root level public_html. I, like many commentors above, feel this is the best solution for its speed and appropriateness; just having an 'assets' directory at the same level as the 'system' one, with images, css, js etc inside. You could use an alias or virtual folder to make things feel better for you...
However, there is a third way. There are libraries that do something JUST like what you want, with the added benefit of Minify (from the accepted answer) and compression, or whatever you fancy. The two libraries I know of are called AssetLibPro and Carabiner, and these allow you to specify an asset path (as you want), and then you load your JS and CSS files (with groups e.g. screen, print if needed). They then serve up all related CSS/JS etc as one file; compressed, minified, cached... whatever you need.