First off, I would worry more about whether or not you want the extra content. The extended versions are, in the opinion of myself and most others, the true and complete versions. Only if you are a theatre purist should you buy the theatrical versions.
That being said, supposedly the extended versions are better mastered, but I've never seen them side-by-side as I only have interest in the complete movies. I can say, though, that the picture quality of the first 2 extended movies is as good as, or better than, anything else I've ever seen on DVD.