Both are fun, depends on what you want.
Sci Fi - you sit in a modified car or picnic bench. You may have to share the car with another group, depending upon the size of your party.
When my 3 DS were younger, we took them to Sci Fi just to keep them occupied watching the movies (I don't think they looked at the food, just shoveled it into their mouths with their eyes glued to the screen)

. We still have the glow in the dark frisbees they served their lunches on!
50's Prime time is a fun place to get harassed by the wait staff, and get some comfort food (meat loaf, fried chicken, etc.). Food is better than Sci Fi, but the experience isn't as unique.
If you want to take a peek at the restaurants, go to Allearsnet.com, click on the dining option, look for the pictures link.
Happy dining!