As everyone as already mentioned no difference in audio or video quality.
MKV - Superior compatibility for streaming to other devices, if you just want the main movie then use MKV.
Folder Structure - Contains menus/trailers/special features - If these matter to you at all then use this, if not then use MKV.
My preference (unlike others) is ISO/Folder Structure, as I like to sometimes view the menus/special features and can still play the main movie if needed, I don't use any other devices so compatibility is not an issue.
Edit - another advantage of MKV is cost, MakeMKV is free where as folder/ISO ripping tools usually are not.