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No, fonts should definitely be under UI control where they are now. Having to change every filetype file just to make the text larger is a bad thing (tm).
No, with colorschemes, you just change one file and it applies to every filetype. It makes no sense to have some parts of the (font) styling like colours and bold and italics specified in the color schemes while other parts like the font face and size to be specified through the UI.
It only applies if the style maker used common styles, maybe the point of the style was to change them all different.
The *best* thing would be to have the color schemes be editable through the GUI (like TextMate, for example), but this is substantially more work.
Somebodys got to do it, plugins are welcome :)
If you could set the font face and size through the colour scheme, you could leave the GUI setting as a global/default that takes effect if not specified elsewhere (ie. in the color schemes).
No, GUIs should always win, or should be set insensitive.
Your suggestion on IRC of allowing schemes to set font size deltas (not absolute values) is a good one, for documentation markups you could make headings one point larger or similar.
Cheers Lex