The default style sheet in Mathematica 9 is different than in 8.
If you still have 8 installed, you can copy its Default.nb style sheet from the 8.0
to the same location in 9.0. Renaming, rather than overwriting, the 9.0 Default.nb is recommended.
You can have both 8 and 9 installed. Before installing the second, change the name of the first to, for example, Mathematica9.app.
I need an example of the fraction parts changing size. A .nb file would be appropriate. Are you using TraditionalForm? Were you used to using OutputForm?
After switching versions, it is good to reset preferences by holding down the SHIFT and OPTION keys as Mathematica starts. Deleting the folder
(home directory)/Library/Mathematica/ is equivalent.
Mathematica looks for /Library/Mathematica under the hard drive and Library/Mathematica under your home directory. Renaming either makes it unavailable.