Remove jQuery and find out what is asking it to be included
I think that it is pretty safe to assume that any module using JS is going to assume that jQuery is present.  Yes they should feature detect this, but its availability in Drupal is pretty much assumed by everyone.  There is no real way to get a list of all of the jQuery dependencies.

CSS can be aggregated and minified if the worry is file count.

If you truly want to manage these yourself, your best bet is to remove the $scripts and $styles variables from html.tpl.php and manage your own, eg $myscripts and $mystyles.  You could also unset/reset them in your own template_process_html.

Drupal is built on hooks.  Don't think of it as having to add code to remove something.  You add code (implement hooks) as a way to modify or extend the default behavior.

Now that I have answered your question, you are really going out of your way to bypass a lot of the power of Drupal.  You should start by looking into what Drupal calls starter themes or base themes.  The Omega and Zen themes are two popular ones.