Well I am by no means a MM expert like some other people are, I don't even like the game that much, but here's my opinion because I too have though this before.
In the end of OoT it shows Navi leaving Link when he's returning the Master Sword. In the beggining of MM he sais he's looking for a "lost friend." Sounds pretty convincing to me that Navi is the one Link is looking for.
So that right there proves why he's looking for Navi. Here's why I don't think he's looking for Saria.
Saria is a sage and even though Saria in the child timeline is not a sage because she doesn't get recognized as a sage until Link turns into an adult, there is a perfectly logical explanation as to why she would recognize herself as a sage when Link is a child. Link goes back as a child to worn Princess Zelda of what's to come in the future with Ganon and such. Well, I propose that Link also whent back to the Kokiri Forest to search for Navi and then ended up getting lost in the Lost Woods (that is where Link started off MM right? I don't actually know just assuming because of this post.) But, before getting lost in the Lost Woods he also warned Saria of what was to come in the future and her role as a sage. So since Link warned her he knows where she is and therefore there is no reason for him to go looking for her. The most logical explanation is Navi.
Please don't get discouraged with your theory though! The beauty of Zelda is finding new ways to explain things and different ideas popping up around every corner! I am by no means a Zelda theorist and I don't even think there is an actual timeline but that's not going to stop me from making little theorys like this. Hopefully an intelligent Zelda fanatic will come along this thread and better explain to you why it's Navi Link is seraching for and not Saria. (or maybe it is Saria
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