It's a common case when one color scheme is good for one filetype and another color scheme for another filtype. It's tough to quickly edit color scheme files manually. So it would be easier to configure each filetype to have it's own color scheme if needed using some gui menu/table.
Also the color schemes management does not work when using, for example, "vibrant ink theme" (http://code.google.com/p/geany-vibrant-ink-theme/), since it overrides filedefs. This issue should be solved in order to be able to switch between such color preferences.