Actually, I'm surprised how much content stayed from SHIII - there's some files that seem to be left over from SHIII assets, just dig around the menu graphics for example and you'll find traces of the old interface that never show up...
There are some notable new additions and some changes; the campaign system, while keeping the same .mis format, is totally revised and split into a lot of different files; textures are DDS instead of TGA; some totally new subfolders have been added like "Shaders"
But otherwise if you knew SHIII's data, you should feel pretty much at home here...
Oh, and as for the config folder and files specifically - exactly the same! I've already done tweaks there as you might have noticed
