Here are my preferences for a good style sheet. They are mainly based on what good published papers or textbook typography looks like.

1) A not too large gradation of font sizes between the largest (Titles) and Text font.

2) Text and Output font size should be the same.

3) Text and Output cells should be unadorned. No frames or color. (In fact, frames are a bad idea for cells altogether.) Then when Input cells are hidden, as in CDF documents, the text and output blend together and read just as in papers.

4) Input cells might have a pale background to distinguish them, Tufte's "Minimum effective difference".

5) Probably a White background, certainly for printing.

6) Openers on the various Section headings but NOT on Titles or Input/Output groups.

7) It might be useful to have a Cell Menu item to toggle between all Input/Output cell groups open, or just the Output showing.

I think you have a valid complaint. In the first place WRI should settle down with their fonts and keep them fixed from version to version. And they should use more taste than they do. How many people like all Red headings in the Default style sheet?

You can always change the font for Text cells. Here are some fonts available on Windows that clearly distinguish between capital I, small l, and the numeral 1: Calibri, Constantia, Book Antiqua, Georgia, Tahoma, Segoe UI (which I think is used in Panels), Verdana,