I've beta tested an app that lets you pre-program waypoints ahead of time. However, even though it's nice to take your time laying out a course without consuming the P3's battery power, I always found it nerve wracking when I let my P3 fly the pre-programmed course, and thus would make sure it was flying very high to clear any unseen obstacles that may be between the points. In fact, I found myself flying the proposed routes manually first--just to make sure I wasn't going to run into anything that wasn't apparently visible on the satellite image maps.
So there is a trade off, but I personally prefer flying the route manually myself so I can see what obstacles I might encounter along a given leg, especially when wanting to shoot scenes that are relatively low.
Yes, if all you plan to do is stay at 400' over a flat Kansas field, then pre-programming would be nice; but there is a legitimate use for programming on the fly--at least you're less likely to enter a typo altitude that buries your P3 into a flat piece of farmland.
Yes, pre-programming waypoints for surveys or SAR would be nice feature to have, but I wouldn't consider this current programming method to be a complete waste of battery power.