This was a Wincest fic, it was written prior to season 4, no Castiel. May have been written in the first season.

Starts at the beginning of the show, with the first episode, but at the buried Native American bones episode Dean talks to a professor that he knows, or something, and, we the reader, find out Dean is really, really smart, and hiding it from Sam. At some point Sam finds a report cart, from when they were children, in a keepsake box that Dean was hiding, that says Dean was a genius, and could have attended any school he wanted. I think Sam confronts him, but I can’t remember. I think Dean stays in contact with a collage professor, who wants, or wanted Dean to get a higher education, because he thinks Dean could be doing something more with his life, and Sam finds out about the calls, and steels Deans phone to call the professor at some point to find out what is going on, and the professor guesses what their relationship really is, when he talks to Sam.

That is all I can remember. Kinda vague, I know, but I loved it, and would love to read it again.

ETA: Found in comments! yay!  thanks