Custom WHMCS API, API
This is something I feel is simple to implement but could work wonders and cut down the need for a hacky addon module with a custom entry-point script.
Right now we can post to api.php or run localAPI. We should be able to as developers have like an add_api_function($id, $functionName) From here it would pass the values given via post or array so we could do actions and then return an array back to be returned to the calling localAPI or outputted via requested format to the web page (api.php).
This would allow so much extensibility and possibilities, its not even funny.
As for the "default" internal API's, you can allow an override or have a check to prevent it, which ever you developer's feel is best.