Just beginning to tinker. Right off the bat - right-click with no ships selected should use mobile behavior - move the flagship to location, with other ships in formation. I like the 'stop and face direction' commands, along with the ability to click-drag waypoints for precise placement. I can't help but think, though, that shield/hit points are too low and manuevering too slow for movement tweaks to be terribly helpful, except with regards to making the correct facing easier to achieve.
In other words, 'stop and face cursor' is wonderfully useful, while waypoints, though I would LOVE them to be useful, are not.