As I keep saying, I am quite sure that the largest part of the increase is due to added functionality.
iMovie being the prime example - just listen to the keynote, and you will know why the size increased so significantly. After all, why should iMovie increase by a few hundred MB just due to the retina upgrade? I am guessing that iMovie contains just a few hundred kb of bitmap graphics (e.g. title screen, icons) which will now be replaced with higher-res graphics.
OK, good. I was worried I was going crazy for a moment. I'm sure there will be a size bump as programs switch over to support the retina display, but I don't think this is going to be anywhere near 2.5 to 3 times as much.