does the D6 version not include the 'exclude' ability / feature?

i am also looking for this.

The aggregation in Drupal 6 is not done by this module. Javascript Aggregator in D6 takes action only after the Core js aggregation. Excluding files form core aggregation is something this module can not influence.

i was thinking more of modules like fckeditor that won't function correctly is their .js files are aggregated. Is there a way to exclude?

Drupal core is aggregating the module files. The Drupal 5 version of this module did the aggregation, version 6 only adds minification and gzipping, which is not compatible with all modules. Javascript aggregator just minifies the file that is aggregated by core and all active modules.

It's not easy. You need to change module's code to exclude javascript aggregation in problematic situations.

For example:

From this:

drupal_add_js($path . '/admin_menu.js', 'module', 'header', TRUE);

To this:
drupal_add_js($path . '/admin_menu.js', 'module', 'header', TRUE, TRUE, FALSE); //last parameter is the key

Can you explain more about how this works? The last parameter tells Drupal not to aggregate the file?

Drupal API - drupal_add_js