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Peter was not specifically a very bright boy. He worked hard in class like all the other terrified Firsties, but his grades never really showed much for it.
He was a bit pudgy, possibly still clinging to the last of his baby fat, so he was already under the thumb of budding bullies. The fat and the bad grades, combined also with his timid stutter and shy attitude, Peter Pettigrew was not a very popular little boy.
And that's possibly why Remus liked him.
Even if he wasn't very good at it, he was dedicated to his schoolwork and he was quiet and when the other kids made fun of him he didn't let them get a rise out of him (at least not until they'd left). The two of them could spend time in the library, the large, dusty, cold room serving as their hang-out as Remus tried to help Peter with any homework he had on hand.
The bullying also isolated the two and Remus was thankful for that. Had Peter not been pudgy or a bit slow on the uptake, he might not have the friend he saw in Peter. He was grateful for that.
Sirius Black and James Potter, his and Peter's roommates, though, liked to try and involve Remus in their play. They were loud and gifted in the classroom and even though Sirius had went through an isolated period at the beginning of the year he and James were very popular with all their classmates.
In the mornings, during breakfast, James would sidle onto the bench next to Remus who was trying to look small and unassuming as possible. He would smile and comment on whatever it was Remus was eating that day. Then Sirius would take the open seat on the opposite side of Remus and the shy young Gryffindor would be boxed in, forced to listen to the two boy's chatter until the bell rang and Remus was able to slip away in the rush of students.
What on Earth would two boys as smart and handsome as Sirius Black and James Potter want with him? Not to mention the fact that both boys were from prominent and wealthy pure-blood families. Peter was a pure-blood as well, but not nearly as decorated as the Black and Potter families. And Remus, he was just a half-blooded werewolf (even if they didn't know the w-part yet).
James and Sirius didn't like Peter, also. They blew off any attempt he made at entering their conversations when they were talking between Remus. The ignored him and even made fun of him in front of him and Remus.
Even though Remus desperately wanted friends who liked him and wouldn't run from or hurt him, he didn't think he could take on the two trouble-making bullies. Their advances for a friendship were started on the wrong path and Remus was made uncomfortable. If his secret was ever to come to light, could he really trust them enough to keep it between them or not hunt him down like the wolf he was so often told he truly was?
Peter was fine for now. He was nice enough, even if he didn't understand some of the things Remus said. And even if he mostly used Remus to understand his homework and didn't really hang out outside of the library and the occasional times they were squashed together on the tightly packed benches during the lunch rush in the Great Hall.