We have eaten at both places a few times. Never had a bad meal at either place, but I have heard people bag on the food at both restaurants. Foodwise, neither one is going to blow your socks off. If you're looking for old fashioned comfort food, you'll find it at 50s PTC. It's my wife's favorite place to eat in all of Disney World. I recommend the pot roast which is really succulent. Meals are very obviously not made to order sometimes. We have been served within minutes of ordering. But they are usually hot, tasty and filling. Food at Sci Fi is a little more hit or miss. But what we have had has always been pretty good. I'd recommend grabbing dessert at Sci Fi over a meal if you just want to take in the atmosphere.
It's atmosphere where both restaurants excel. 50s PTC is just a fun place it sit down and relax. You can play along with the staff which is fun. They do not typically give anyone a hard time unless the guest is playing along. So don't worry about that. It's all in good fun. We always get a few good chuckles. Some waiters have had us laughing through our entire meal.
Sci Fi has a more elaborate theme. It's cool to eat in a car. But with that comes some drawbacks. For one, it is really dark. It can be hard to see what you are eating. And if you do get seated in a car, you won't all be facing one another which can make conversations difficult. If you want to be able to carry on a conversation with everyone, I recommend 50s over Sci Fi.
In terms of nostalgia, they both have it in spades. Sci Fi is a little more specific about the type of nostalgia whereas 50s PTC is a bit more general. Overall, I give the edge to 50s. But I'd recommend either for a fun dining experience.