Example of how to add a custom 'Recipient' shortcode to the messages system, this adds a [RECIPIENT_ATTENDEE_ID] shortcode which parses to the recipients EE Attendee ID.

ee_messages_custom_recipient_shortcode.php

<?php //Please do no include the opening PHP tag if you already have one.

/* This filter allows you to add custom shortcodes to the message system
 * $shortcodes is an array of the available shortcodes for the current library
 * $lib is the current shortcode library
 */
function ee_register_new_custom_messages_shortcodes( $shortcodes, EE_Shortcodes $lib ) {
 	//Add a shortcode to be used with the EE Recipient within messages
	if ( $lib instanceof EE_Recipient_Details_Shortcodes ) {
		//Add your shortcode to the add as the key, the value should be a description of the shortcode.
		$shortcodes['[RECIPIENT_ATTENDEE_ID]'] = _('This is a custom RECIPIENT shortcode!');
	}
	//Return the shortcodes.
	return $shortcodes;
}
add_filter( 'FHEE__EE_Shortcodes__shortcodes', 'ee_register_new_custom_messages_shortcodes', 10, 2 );

/*  
 * This filter allows you to hook in to the shortcode parser, check for a shortcode added above and return a value for it using the data passed to the parser.
 * $parsed are the current values being parsed.
 * $shortcode is the current shortcode passed to the parser.
 * $data is the current data available, this can be different types of objects depending on the parser.
 * $extra_data is a collaction of various data available within the messages system.
 */
function ee_register_new_custom_messages_shortcodes_parser( $parsed, $shortcode, $data, $extra_data, EE_Shortcodes $lib ) {
	//Check for the EE Recipient Details shortcodes library as that's one of the libraries we added a custom shortcode to above.
	//$data or $extra_data will be an instance of EE_Messages_Addressee which can be used to pull the required details.
	if ( $lib instanceof EE_Recipient_Details_Shortcodes ) {
	    
		if ( $shortcode == '[RECIPIENT_ATTENDEE_ID]' ) {
		    //Make sure we end up with a copy of the EE_Messages_Addressee object
	        $recipient = $data instanceof EE_Messages_Addressee ? $data : null;
	        $recipient = ! $recipient instanceof EE_Messages_Addressee
	                            && is_array($data)
	                            && isset($data['data'])
	                            && $data['data'] instanceof EE_Messages_Addressee
	            ? $data['data']
	            : $recipient;
	        $recipient = ! $recipient instanceof EE_Messages_Addressee
	                            && ! empty($extra_data['data'])
	                            && $extra_data['data'] instanceof EE_Messages_Addressee
	            ? $extra_data['data']
	            : $recipient;

	        //Confirm we have a valid receipient
	        if (! $recipient instanceof EE_Messages_Addressee) {
	            return '';
	        }

	        //Confirm we have a valid EE_Attendee object
	        $attendee = $recipient->att_obj;
	        if (! $attendee instanceof EE_Attendee) {
	            return '';
	        }

	        return $attendee->ID();
	    }
    }
	//If not within the correct section, or parsing the correct shortcode,
	//Return the currently parsed content.
	return $parsed;
}
add_filter( 'FHEE__EE_Shortcodes__parser_after', 'ee_register_new_custom_messages_shortcodes_parser', 10, 5 );