Apart from the size of the new boxes, are there any differences on the discs? Have Fox not included all the extras from the original set?

Sadly, the extra features discs from the original (and wildly overpriced) DVD sets have not been retained on these new slimline case reissues. Still, the episode comentaries, deleted scenes and occasional special effects clips are still there, and the documentaries that were included on the original sets were pretty lackluster, so don't feel too bad and just pick up the new sets.