Professor Kaye,
Thanks so much for taking the time to give your thoughtful comments.
I heartly agree with your view concerning the superiority of integrating mind-mapping, note-taking, and writing. In fact, I'd additionally like to see full bibliographic management integrated into the mix, so a student has a truly central point for doing the bulk of his or her work. Could Zotero, for example, cite into NoteCase, or most anything else? (Answer: Yes, it could, the pipes just need to be written.)
I looked closely at NoteCase when I was making UberStudent 0.9 about three years ago, and did open a dialog with Miroslav Rajcic at that time. I included a "lite" version of NoteCase in that version, as default, along with a hyperlink in the menu to obtain the full version. That was as far as things could wind up at that time. Your comments, however, have spurred in me some new ideas I'd like to submit to Miroslav. I promise I will write to him shortly after I get new 32-bit versions of UberStudent out (I'm testing a 32-bit build of the XFCE Edition presently, and am writing from it right now).
I looked closely at Cherry Tree when I released UberStudent 1.0 two years ago. I deemed KeepNote a better alternative at that time. Given your comments, it appears the former has undergone some hightened development since then. I'll take a new look at it as soon as I finish writing this. I can for sure attest to Giuseppe Penone's responsiveness as a developer. The reason X-tile works in UberStudent or in anything downstream of it is because I asked him for a fix to his program's AppIndicator docking behavior.
I will keep you posted on these matters and very much welcome your continued input.

Others reading this: what are your thoughts?