David, I agree with you, there are some side effect modifying any of the Mathematica' system file. However, such changes are in general very easy and users may want to adjust their own copy. As you suggest, the same change can be done in a private stylesheet, but this means the changes have to be done for any new notebook or, if you save a personal stylesheet, you should associate the new stylesheet to any new notebook. Finally, it is also possible to set the new default stylesheet to be your own stylesheet, but all these alternatives will still have the issues you are referring too: other people will not have your personal stylesheet on their machine or a new Mathematica version will require the same operations.

Another way is to apply a change to the native Core.nb Stylesheet. Note that normally this document has two options not allowing its modification. These are basic steps: 1) open folder where system's stylesheet are installed. In window it should "C:\Program Files\Wolfram Research\Mathematica\10.0\SystemFiles\FrontEnd\StyleSheets" 2) open the Core.nb file with Mathematica 3) Open Option Inspector and set "Show option values" on "Core.nb" and 4) search for Editable and set the value to True, search Saveable and set the value to True and close the Option Inspector 5) in the Core.nb search for the section "Style for Mathematica System-specific Elements" 6) then search for the subsection "Default Box Styles" 7) search for style definition named "Graphics" 8) change FontFamiliy to "Times" 9) close and save the Core.nb 10) Open Core.nb once again and set Editable to False (Saveable option cannot be set back to False).

This should work for all new notebooks.

I wish I could curb (at least for my own material) Mathematica's drift toward sans-serif fonts everywhere. I find them a big step backward in legibility.