The major changes in DKS versus the original ED are

a) Flying fortress levels are completely different
b) Most anti-dragon zones (the red auras) have been removed
c) In a lot of places enemy placement has been modified, especially in the latter parts of the game (e.g. Oroboras fjords)
d) Loot balancing has been radically changed
e) Difficulty spikes have been addressed
f) Major graphical overhaul
g) A variety of mechanic changes should make combat feel better (e.g. no homing missiles, level difference not that important anymore when dealing with enemies)
h) A whole bunch of usability changes (which are also present in FOV)

DKS was intended for people who never played ED before, but it does offer a better experience than ED in my opinion. However, if you want to continue playing with your existing savegames, then you should get FOV. A lot of the improvements of DKS are present in FOV, and the only ones that are missing are the ones that couldn't be intrdouced without breaking savegame compatibility.