We have been to both restaurants you listed, but I voted for Sci-Fi.
I don't really think one place serves better food over the other. In my opinion anyway. But I do prefer the atmosphere of Sci-Fi.
50's Prime Cafe is one of those restaurants that we wanted to try once. We did, but it's nothing so special that we'll be returning.
I could see us going back to Sci-Fi maybe just for appitizers and deserts. We did the lunch thing during our visit, and I think their hamburgers are way over priced for what you get. But I do love the atmosphere enough to return for some snacks.
Diznee25