For the BoG Arc, I vastly preferred the movie, though I did enjoy the universe level clash giving a good idea of the sheer scale of the Gods compared to previous characters, even if it were likely to just appease the VS fanboys. It was quite enjoyable manga-wise though, seeing as how it wasn't dragged out without necessity.
Super's version of FnF was a vast improvement, however, seeing as how several unexplained events from the movie were given some light, such as Shisami's massive gains, or in Super's case, Tagoma's. Piccolo dying also increased the sense of severity, even if at this point, death in DB is meaningless.