I have seen both the iBooks and Kindle version now. The iBooks version's video is definitely of a much higher quality.
Take for example the video of the ending of ROTJ with the alternate music track. The iBooks version is 720p video. The Kindle verson is dvd resolution video with a lot more compression.
The Kindle version is 8.5mb
The iBooks version is 66.6mb
The iBooks version however has DRM'd video.