I've been to both many times, and for me, it's 50's Prime Time Diner all the way. The Sci-Fi diner ambience is great, but their menu and food is simply unforgiveable. It's almost incomprehensible to me that they allow such a unique and potentially great venue to serve such utter junk. Heck, i'm fine with a simple burger and fries concept, but how hard is it to make a good burger ? Sci-Fi also makes it a little tough to carry on a conversation over a meal.
The 50's Prime Time has much better food, IMHO, and when my kids were around 10, they really enjoyed the "interactive" element of having a dinner at "mom's". In fact, my oldest still relates with glee the time he got a sticker for being in the "clean plate club".
As an added consideration, if you enjoy a nice adult beverage now and then, like I do, Prime Time has the advantage of a full stocked bar and a much better beer selection than Sci-Fi.