Choosing between these two spots is more about the experience than the food. If you like dining in a mock-nighttime setting, similar to the Blue Bayou in Disneyland, while old-time horror trailers are playing on the big screen, then Sci-Fi is right for you. If you enjoy dining in your mom's kitchen while the waitstaff screws with you about cleaning your plate and taking your elbows off the table, then 50's is the place.
I dined at 50's once a few years ago, and it wasn't a good experience. The "cousin" that was waiting on me didn't know when to stop, and moved from fun tweaking into hard harassment. I was a tired park stormer, and didn't appreciate not being able to relax and enjoy my dinner without constant nagging. Others might be into that, but it didn't work for me.