My vote is for Sci Fi. We always get milkshakes, burgers and fries and love it! I have read reviews that anything other than burgers and fries are not so good. The atmosphere is great! Look for the hidden Mickey in the cartoon.
We did the 50's PT once--we had a terrible waitress. We really did not like the food--I am sure things may have changed since it was about 5 years ago.
We've done both and we would say 50's Prime Time. We had a bad experience at Sci-Fi, but maybe it's time to try it again. No time on this next trip but, there is always future planning!
We like Sci-Fi better. The kids liked the movies and the food wasn't bad. We did the 50's years ago and it was ok, but we don't really like pot roast or fried chicken, and not big into the interacting stuff they do.
50s has many more enjoyable menu items than does Sci-Fi. Sci-fi is more of a lunch thing to us. A place to grab a nice burger and onion rings. But 50s is a place to enjoy a nice, savory meal. Nothing fancy, of course, but tasty.