It really all comes down to the reader's preferences really. Who a person would like to see as the seme and uke.
I guess I would run more along the stereotypical line of the shorter and more hyperactive of the pair as the uke just because I like that type of character as the submissive one. In this case, my preference would be Naruto as the bottom and Sasuke to be the top just cause I can easily see the pairing going that way. I personally love the challenge of trying to keep the character 'in character' as much as possible as I'm writing a fanfic though. Though but fun
But if the story is well written though, I might make an exception and read a SasuNaru