With mathspec, when you change the math font to an OpenType font, the spacing within equations is not fine: it is the same than the text mode spacing. For example in the equation $e^j$, the 'j' will collide with the 'e', most of time. So with mathspec you have to type $e^{"j}$ to space the 'j'. This is refered as the 'glyph bounds' problem in the mathspec doc.
What is really too bad is that it breaks compatibility with LaTeX.
Is there any way to both have correct spacing AND compatibility with LaTeX?
Here is an example with two clashes :
\documentclass{article}
\usepackage{mathspec}
\setmathsfont(Latin,Digits){Times New Roman}
\begin{document}
$e^j + |f|$ should be written $e^{"j} + |"f|$.
$\"abcdefghijklmnopqrstuvw"$
$abcdefghijklmnopqrstuvw$ : the spacing is too thin, suitable for text, not for math.
\end{document}

$e^j$with the default math font (Computer Modern), I do not get a clash between theeand the raisedj. Incidentally,$e^{"j}$produces the exact same output on my system as$e^j$does. Are you maybe using a non-default set of math fonts and/or babel with a non-English language setting? – Mico Aug 24 '11 at 15:08