I think it depends on what you are looking for. We have two older boys (pre-teens) and a pre-schooler, and we've been to both.
Sci-Fi is fun, but our pre-schooler doesn't recognize any of the movies and, therefore, is only moderately interested. He did like the cars, but he sat in the same row as my husband and me, so it was a little crowded. We like the lunch items at sci-fi, but were not crazy about dinner. Because of the way sci-fi is set up, it feels more like an attraction than a meal. We can't really talk with our kids there because the two older boys are in front of us, and our pre-schooler is really interested in checking out the car. I think if we had a car closer to the screen, he might have been more interested in it! We'll return for lunch next trip, but it wasn't at the top of our list. More like: "we'll be in DHS that day, and we already have ADRs for Brown Derby and 50's, where else should we go?"
50's was great fun, and we think the food is really, really good. Everyone was happy with the food (and that doesn't happen every day!) I had the wedge salad and shared the pot pie with our oldest son, and it was outstanding. The "show" was goofy and fun. I don't generally like Ed Debevics, but I liked this. Maybe it's because everyone is just in such a great mood at Disney! Anyway, the seating there is more traditional than at Sci-Fi, so we could talk at lunch. But they do have TVs on, so the kids would float in and out of the conversation. Our pre-schooler loved the old TVs and enjoyed his kids' meal. We'll definitely be back next trip!
If we had to choose between the two, we would all vote for 50's.