One of my favorite things about Merlin's and Arthur's relationship is how it transcends their roles: they become friends even though Arthur is a prince and Merlin a servant. Accordingly, I'm not very fond of stories in which the characters blithely assume that of course Merlin will bottom for Arthur, and in which Merlin proceeds to do so forever.

(On the other hand, I love stories in which Arthur makes that particular assumption and Merlin either 1) smacks him upside the head for being an entitled prat, or 2) says, "All right, if you're going to make such a fuss over it. I kind of prefer being on the bottom anyway.")

I'm not sure if that's the entire reason I prefer Merlin topping Arthur--sometimes pairings just resonate for you a certain way, you know?--but it's certainly a large part of it.