You have motivated me, I have clients that don't need "Jetpack", they want to see their Stats, and they don't want it to shift in the menu structure, they are not geeks like us, and have enough trouble using the Internet as is.
I had made a start on a plugin last month that would adjust the menus, but it overwhelmed me, so put it aside.
So right now I have applied this quick hack/fix, that will adjust the menus, for others who would like to apply it;
Move Jetpack to "Tools"
EDIT: jetpack-lite\jetpack-lite.php approx line 597
$hook = add_menu_page( 'Jetpack', 'Jetpack', 'manage_options', 'jetpack', array( $this, 'admin_page' ), '' );
$hook = add_management_page( 'Jetpack', 'Jetpack', 'manage_options', 'jetpack', array( $this, 'admin_page' ), '' );
Move "Stats" back to Dashboard Submenu
EDIT: jetpack-lite\modules\stats.php aprrox line 189
$hook = add_submenu_page( 'jetpack', __( 'Site Stats', 'jetpack' ), __( 'Site Stats', 'jetpack' ), 'create_users', 'stats', 'stats_reports_page' );
$hook = add_submenu_page( 'index.php', __( 'Site Stats', 'jetpack' ), __( 'Site Stats', 'jetpack' ), 'create_users', 'stats', 'stats_reports_page' );
NOTES:
http://codex.wordpress.org/Administration_Menus
http://codex.wordpress.org/Function_Reference/add_menu_page
http://codex.wordpress.org/Function_Reference/add_submenu_page