The power of TheBrain lies in tuning it to your own needs. I.e. I second others in thinking that automatic import into TheBrain is not a good way forward. We have automatic import into other programs, like Endnote you have mentioned. This is a perfect program for reference management when you write your papers, and I use it for exactly this. However, linking ideas between articles in TheBrain, this is work you need to do by hand because that is where you tune your system, where you input the data in such a way that you will find them in the future.
The system you have presented in the small brain is way too complicated to maintain over years. I work with pdf's I label with year, journal, mainauthor (1993, JPerkinTrans1, Haines). This I link to the author's name and the field keywords. As children I have the title (a type, different color) and the main messages of the paper as individual thoughts. After having linked more than a thousand papers, it still works and I find very interesting connections. But, you have to put in the work.