I have been to both on two seperate vacations, neither is a great memory but I will tell you about my experience and let you decide for yourself, but I would say neither.
First 50's Prime Time Cafe~ I went on Thanksgiving Day in 02 with my family(Mom, Dad, 3 Sisters, 2 Bro-in-laws and one niece). Now let me explain that we are short people, Im 5'3, lots of resturant I can not sit comfortably in the seat without putting one leg under my body one to boost me higher to the table and to because I can not stand that I can not touch the floor with my feet. The CM was playing fun but made me feel 1 ft tall telling me to put my feet on the ground. Also if you dont finish your food there are some who will try to playfully try to force feed you. Plus overall, none of us except my niece who was 3 was impressed with the food.
Second Sci-fi~ I went on my Disneymoon in Sept 06 with my DH. We enjoyed the enviroment, it was very neat. However, it is very dark and hard to see your food. Another thing is we are both smaller at the time I was 115 and hubby 150 and we were crowded in the seats. We were most disappointed about the food. Not very good. My mom, dad, grandma and niece(Different niece(4) went Feb 08 and said they did not enjoy the food either. (when they told me they were going, I did not tell them we did not enjoy our food). They went to Hollywood and Vine and said its very good tho.
Hope this helps.