The flying fortresses were redesigned in DKS, getting rid of the generators and most of the anti-dragon zones.
That sounds like a definite improvement to me: the forts for me were one of the less enjoyable parts of the game, especially Kali's (I think - the "green one", anyway) with it's eleventy billion generators, not all of which I could find last time through in spite of spending hours searching for them. I think I'd approach them with a lot less trepidation if I knew I could be in and out, just getting on with stuff that needs doing: although I normally like to spend my time doing things, disabling the generators was something I found quite tedious.
Probably the closest I came to something similar elsewhere was trying to close all sixty gates in Oblivion (I think I found 57 in the end). I don't recommend it!