First of all -- YAY

for your first trip to WDW!! How exciting!!!
Secondly - to answer your question...
Like previous posters have said, I think it really depends whether or not you want to "watch the show" or "be in the show." DH and I have eaten at both and we've had a great time at both!
I would have to say, though, that the first time we ate at Prime Time, it was just the two of us and the interaction wasn't as "good" as it was when we ate there as a group of five (my mom, dad, husband, brother-in-law, and myself). So, if you have a group of people (more than two, probably), then you will have a GREAT time at Prime Time!
As for the food, I would say that Sci Fi caters more to the "soup and sandwiches" kind of thing while Prime Time caters more to the "comfort food." You should probably check out the menus on
Allears.net and see if one menu appeals to you more than the other.
Regardless of whichever you choose, I
know that you will have a fantastic time!