This is hard question because it all depends on your party. Do you have young children, older kids, no kids. Also how many in the group.
So this is what I have experienced at both.
Sci-fi is a super cool restaurant with indoor 1950's drive thru theme. It is a special experience to dine there just for the atmosphere alone. The food is ok, nothing to rave about. My problem is that at the car tables, you can only be seated by two. And none of the party is facing each other so forget having a conversation. Next problem is that it is crazy dark in there so if travelling with a baby or young child, it is too dark to see him properly and trying to feed your child in the dark is a nightmare. Also, the high chair can only be put on the outside of the car and it is very awkward. I also have to say that the B-movies they show scared my then son who was four at the time. The food has been, on average, not that great either, but we seem to keep going back despite all that because it is just too cool of an atmosphere.
50's Prime Time has a fun atmosphere also where you feel like you stepped back in time into a 1950's kitchen with checkered floors, tacky wallpaper and old TV sets playing black and white sitcoms. The food has been consistently good there and I love their milkshakes! The waiters play a little with the guests but in my experience nothing offensive. I find it entertaining. The main reason I like it is that the food is good home cooked comfort food and it is a place where you can just relax with the kids.
I really like both so I always go to Sci-Fi for lunch and 50's for dinner. QS at HS is always bad anyway so I do 2 sit down meals on my HS days.
Hope this helps