If I might give my opinion on which features PubPub should implement next:
- adding "Math in-line $$" in Formatting menu
- enabling upload of LaTeX files
- enabling upload of PDFs, to store on PubPub existing research (combined by via.hypothes.is, one can annotate PDFs, which is in the spirit of PubPub)
- include some interesting features of SJS like grading, download as PDF, add to personal library...
I am impressed at the job you've done for a graduate project ! Best wishes :-)