Drupal 7 js compression generating 6 files
Surprisingly, the larger number of files can actually save bandwidth on subsequent requests, something that YSlow doesn't take into account.  Aggregating everything into a single giant file is really only optimal for visitors that load a single page and no others.

I wrote an article explaining the details in Drupal 7: Taking control of CSS and JS aggregation.

To reduce the number of files, you can try the Core Library module. The article above also has some example code that will group the files together using hook_css_alter() and hook_js_alter().