That's a good idea.
I've actually added a separate request for the superscript/subscript format in nodes/thoughts: http://thebrain.uservoice.com/forums/4597-thebrain-feature-suggestions/suggestions/2863506-allow-superscript-and-subscript-formats-in-thought

I was actually thinking mainly about formatted node/ Thought bubble text in my feature suggestion... though I don't think that was very clear.
I agree, it would be easier if people could just create and edit cleanly formatted mathematical notation via keyboard shortcuts. I actually really like the way Mathematica handles input of formulas and special characters. (there are menus to place fractions, superscripts, integrals etc. but most of the formating can be done via shortcuts or short escape codes) What mainly bothers me about the Microsoft method is that I have to do everything with the mouse. Having to search through the multiple menus every time I nave to put together a new formula gets annoying pretty quickly.
The way I imagine it, the formatting could be done via LaTeX in the background with something close to the Microsoft Word or Mathematica input interface/functionality shown in the foreground. Users could then switch the view to look at and edit the LaTeX code directly if they want.

Yes, the Microsoft Word 'insert equation' feature can get a bit dodgy. But if LaTeX display functionality is going to be implemented, it would be easier for people if they, for example, pressed a button or two (ctrl + /) that would insert a 'fraction template' (shift + 8 to multiply (*)) and then click in the numerator and denominator boxes in the template to type in numerator and denominator - much like in a Ti-nspire CAS calculator. If they are able to do this instead of having to type in the LaTeX code, more people, especially those who are unfamiliar with code format, will be able to easily use a TheBrain feature that is flexible and is able to let them insert any type of equation.
To add to that, I would suggest if the superscript/subscript functions were to work in the thought bubbles and not only in the notes so that people can put an exponent to a number (superscript) instead of typing (x^2) - this is messy and confusing.

This would be an immensely helpful feature for anyone who might want to use this program to store information that is mathematical in nature.

I would actually suggest implementing LaTeX display functionality... maybe in addition to the Microsoft Word 'insert equation' feature. (LaTeX is more flexible/powerful than the Microsoft equation editor but also a bit more difficult to get into)
I actually just added a separate request concerning the implementation of LaTeX:
http://thebrain.uservoice.com/forums/4597-thebrain-feature-suggestions/suggestions/2840921-extend-text-formatting-options-with-latex