We have done both Sci-Fi and 50's, and found the food and theming is great at both. However, I would cast my vote for Sci-Fi.
I'm not sure if you have kiddos in your party, but when we went to 50's, we had sort of an unusual experience. Our waiter was very nice, but pretty intense. He called himself Cousin Ryan, and he was pretty into the whole "hey, you're part of the family/make yourself useful/mind your p's and q's" concept of the restaurant. We had a good natured back and forth with Cousin Ryan during our meal, and our food was very good. I can't remember exactly what my youngest son ordered, but I know it came with corn, because towards the end of our meal, Cousin Ryan gave him a hard time about not eating all of his vegetables. Cousin Ryan scooped up a spoonful of the corn and fed it to my son. My son laughed nervously and ate the corn, but then was quiet the rest of the meal and begged to leave. Once we had settled our bill and left 50's, he started crying and said he didn't want to eat there again, because it was embarrassing being made to eat his food.
To be clear, we had no idea that our kiddo felt this way. We all thought it was fun to have the back and forth with our waiter, but it really made my son uncomfortable. If it were just my hubby and me, we'd definitely go back to 50's. We enjoyed the good natured ribbing from our waiter, and the food was good. However, when we have family trips in the future, we've promised our youngest we won't go back because of this experience.
As for Sci-Fi, we find it to be a really good "escape". It's dark and quiet, and it's a nice respite from the heat and crowds of the parks. The times we have been there, we find it relaxing to just sit, chill out, and watch the silly movies. The food is good, and we leave feeling refreshed and ready to have more fun in the parks.
Just thought I would share our experiences. Either way I'm sure you'll have a magical time!!