The special features are completely worth the extra cash IMO. In fact they are the only reason why I never even considered selling off my old season sets to pick up the newly packaged ones, despite the fact that they look cooler and save space.
I'm just not a fans of prequels really. I've actually never seen one that I liked because it takes away so much from the unkown. You know that Mulder and Scully won't be in any real danger, nor will any of the secondary characters such as the LG, CSM, Skinner, and Doggett die because we already...
As much as I would love to see the LG back in the sequel, it would just be too cheesy if they "found a way" to show that they never died or something to that extent. Same goes for Krycek and CSM. Unfortunatley they are all going to have to be restricted solely to flashbacks if they are to appear...