In this revised solution, there is a 2pt gap above the bar and a 4 pt gap below it, as specified in the optional arguments to \stackon and \stackunder respectively. Obviously, those numbers can be tweaked (even to the point of being made negative) to deal with the specific characteristics of your font. If you want the division bar raised relative to the horizontal math axis, then the .5ex argument of \raisebox can be changed.
EDITED to load \ifthen package explicitly, since it is no longer done automatically by stackengine.
\documentclass{article}
\usepackage{stackengine}
\usepackage{ifthen}
\newlength\testwida
\newlength\testwidb
\newlength\mywidth
\newcommand\newfrac[2]{%
\setlength\testwida{\widthof{$#1$}}%
\setlength\testwidb{\widthof{$#2$}}%
\ifthenelse{\lengthtest{\testwida>\testwidb}}%
{\mywidth=\testwida}%
{\mywidth=\testwidb}%
\raisebox{.5ex}{%
\stackunder[4pt]{\stackon[2pt]{\rule{\mywidth}{.4pt}}{$#1$}}{$#2$}}%
}
\parskip 1ex
\begin{document}
\(x^3 \, \newfrac{x + y^2}{\sqrt{xy}}\)
\end{document}

ORIGINAL SOLUTION:
If I am understanding your problem, your font is causing "unnatural" vertical spacing. If that is so, you can use the stackengine package to stack the items with any particular gap (above and below the crossline). In this example, I show the gap as the default (3pt), then as 1pt, and finally as 4pt. EDITED the answer to get the math axis correct.
\documentclass{article}
\usepackage[oldsyntax]{stackengine}
\usepackage{ifthen}
\newlength\testwida
\newlength\testwidb
\newlength\mywidth
\newcommand\newfrac[2]{%
\setlength\testwida{\widthof{$#1$}}%
\setlength\testwidb{\widthof{$#2$}}%
\ifthenelse{\lengthtest{\testwida>\testwidb}}%
{\mywidth=\testwida}%
{\mywidth=\testwidb}%
\raisebox{.5ex}{%
\stackunder{\stackon{\rule{\mywidth}{.4pt}}{$#1$}}{$#2$}}%
}
\parskip 1ex
\begin{document}
\(x^3 \, \newfrac{x + y^2}{\sqrt{xy}}\)
\Sstackgap=1pt
\(x^3 \, \newfrac{x + y^2}{\sqrt{xy}}\)
\Sstackgap=4pt
\(x^3 \, \newfrac{x + y^2}{\sqrt{xy}}\)
\end{document}

[EDIT: The second MWE uses obsolete stackengine syntax for setting stackgap lengths (e.g., \Sstackgap=1ex), which prevented scalable lengths from scaling under a fontsize change. Version 2 of the package (submitted 7/11/13) remedies the problem with a small syntax change.]
.texfile, starting with\documentclassand ending with\end{document}? Then I can paste it into my editor, reproduce your situation on my machine, and start thinking about a solution. – John Wickerson Jun 25 '13 at 10:26\mathchoice, or set a different\fontdimen22. – egreg Jun 25 '13 at 10:40\begin{document} $$ \bigg(\frazione{a+b}{c-d}+\frac{a+b}{c-d}\bigg) $$ Here, raising the whole fraction on the left seems have no--sense, but using symbols from {\sl mathematical pi font/} (which I can't load here because they belong to my local tree), I need to do this. \end{document}`
– Martino Jun 25 '13 at 11:40\fontdimen22for the font you're using for the math symbols; however, without an example of your setup it's difficult to say how. – egreg Jun 25 '13 at 13:02