add reference management capability (interface with EndNote, Citavi, Zotero, etc.)
Something along the lines of Sciplore (See Sciplore.org). But, rather than tying the reference management to the plex, create an interface or somehow program PB to link & talk to programs such as EndNote, Zotero, Mendeley, Citavi). This'd be a huge boon in academic research.
Qiqqa seems to have much more robust features in the reference management side of things, it's a shame that their mindmap feature ("brainstorm") is so difficult to use that I have given up on the software.
It seems to me that TheBrain is a much better start, and it would be relatively easy to integrate the kinds of functionalities that are in Qiqqa, Mendeley, and other reference managers. Unfortunately, it doesn't seem like their development team is very active in this forum.
Don't forget Papers 2...
Reference managers are great for storing/sharing/citing papers. I use the Brain for seeing connections between papers and people etc.
A link between a reference manager and the Brain would make the data management faster/easier and would allow me to focus on the data and not on inputing the references themselves...
Anthony Queen commented
I would also consider integration with Jabref (Freeware) in addition to those already mentioned