Yes this is a great deal for a great film. For those who haven't seen it, don't think it's all guns-blazing action, this is actually a thinking man's anime, much like the Patlabor movies. A couple of action scenes bookend the movie, but it's all about the relationship between a man and a girl at opposite ends of a war.
It's use of Red Riding Hood and the Big Bad Wolf as a metaphor is about as subtle as a 2x4 to the forehead, but it's still an interesting and original animated movie.
You aren't missing much by getting the standard version, the SE has the soundtrack which I never listened to as well as a featurette disc which was a little too modest with it's information.
Jeremy