We like the food at 50's better, but the theming at Sci-Fi is by far the best on property. In fact, I almost say not to do Sci-Fi for your first meal because it will set your theming expectations way too high. Also, it depends on who is in your party. There have been people who have said that sometimes the movie clips can be a little intense for very young kids. If you are planning on 2 days at DHS, I'd go with 50's first and then Sci-Fi. If you are only spending one day at DHS, go with Sci-Fi.
If you haven't made ADRs yet, if you are picky about timing you may not have too much of a choice.