I want to keep my notebook magnification at 125% yet increase the
overall appearance of everything. Is there an easy way to do this, as
I don't want to increase the font sizes?
You can achieve this by increasing the default Magnification (one way to do it is to evaluate SetOptions[$FrontEnd, Magnification -> 1.25]) and at the same time reducing the default font size by specifying a custom Private Notebook Stylesheet. The latter is more complicated but I can give you an example of a Private Style Cell from which you can start (it controls the Magnification in an independent way):
Cell[StyleData[All],
Magnification->1.25,
FontSize->7]
