This video sums up quite well a lot of the changes that should be made (although he is very harsh and I don't agree with everything he says, I didn't mind the ads on the boards for one). The main things are the bloom lighting, animations, atmosphere and the sound mixing at times, especially during certain cutscenes.
One other thing I would personally say is a lot of the areas from the old games didn't transfer well to the New n Tasty style camera and I would say that the best part of NnT gameplay-wise was definitely Alf's Escape. That whole section felt like it was built with the new camera mode in mind and thus it seemed to fit the new game more than a lot of the revisted areas. So yeah in Soulstorm make sure the areas are built to work with the new camera system.
I imagine going through this thread it might seem like people weren't too keen on the game but I for one want to say (and I'm sure most here will agree) that NnT was still brilliant, but it's better for us to be honest about the bits we weren't too fond of so that Soulstorm will be a better game all round!