We find the food at both to be pretty much lower end chain restaurant (think Applebee's). The unique atmosphere of Sci Fi just can't be beat for us.
When we went to 50s, we didn't get a server who interacted with us much at all...I mean not even the level of a regular restaurant interaction, much less any shtick. It does have that retro 50s look, which was cool for DH and I (in our 30s), but my kids didn't really get it because they don't watch reruns of old shows. Whereas, while my kids don't understand a drive in movie, they understand eating in a car that feels like it is outside and the fun movie clips. Sci Fi is also dark and quieter, while it doesn't lend itself to family conversation, I find it a nice break. It is also nice that you don't have to see or really hear all the people waiting to get in while you are eating.
ETA: We ordered the pb&j shake at 50s. It just tasted like a shake made with peanut butter ice cream. Actually, tasted like it was made with ice milk/lowfat ice cream or not blended well because it was icy in parts. It was fine, but far from the best dessert or milkshake even at WDW.