A general theming system is unlikely to appear but the next version under development (220.127.116.11) does offer more configurability of colors that might be limiting you today.
// Add "fiddler.inspectors.RequestHexView.HeaderColor" and "fiddler.inspectors.ResponseHexView.HeaderColor"
// Add "fiddler.ui.Colors.IsHTML" "fiddler.ui.Colors.IsScript" "fiddler.ui.Colors.IsAuth" "fiddler.ui.Colors.LoadedFromSAZ"
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