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If you don't mind "destroying" the font sizes for things like the copyright page, table of contents, etc. you can open the .css file(s) and remove all font-size: lines with a regular expression. For novels the only part of the book that matters to me is the chapters; there aren't any footnotes or figure captions or whatnot that should be a different size.

You can also preprocess the book by using calibre's convert book thing and convert it to the same format, and set up the conversion parameters for something you like. Even though it says it will normalize the font size (I use 1em) there are still places where it leaves the original, or something. After I do that then I remove the font-size: lines. I'm using a Kobo so almost all of my books start out in Kindle format and I use calibre to convert them to epub. Doing this conversion is also required for the really brain dead formatting where they've embedded style= lines in the html; calibre will move all of that into the .css file.