I just compared MkII and MkIV in this respect, and the MkII fraction
looks more symmetric (more correct) than the MkIV version.

Here is the MkII code:

\usetypescript[palatino][ec]
\setupbodyfont[palatino]
\starttext
\startformula
{3\over4}\quad {1\over2}
\stopformula
\stoptext

I've attached  (cropped) images to show the difference.

Another difference is in the fonts.  For the MkII version, pdffonts gives

  IVJLXF+TeXGyrePagella-Regular        Type 1            Custom           yes yes no       4  0
  IVJLXF+TeXGyrePagella-Regular        Type 1            Custom           yes yes no       5  0


For the MkIV version, pdffonts shows a math font (maybe for the
thicker fractional bar):

  EUEJAR+TeXGyrePagella-Regular        CID Type 0C       Identity-H       yes yes yes     18  0
  UPBTGS+TeXGyrePagellaMath-Regular    CID Type 0C       Identity-H       yes yes yes     19  0


If you have suggestions for how to change, slightly, the numerator and
denominator placement when using alatino, let me know.

Maybe the entire problem is that the division line is thicker in
Palatino math than in the text font, and maybe sits below the math axis
(so it gets too close to the denominator)?

-Sanjoy