Let me start with a screen-grab:
It is clear from the start that colors were not chosen with logic in mind. The V6 icon for Eeschema should have the transistor in red; the same as the two resistors in the icon. The traces in the icon should remain the default color for what happens when a wire/line is drawn in the schematic.
I would suggest to change the top resistor to a top capacitor; because it appears that two parallel red lines would fit. Then the schematic icon would show a resistor, capacitor, and transistor all off the same color.
Then make the default color for the body outline of schematic symbols the same color red (or other) in both Eeschema and the library editor.
Change either the transistor in the schematic editor to an OpAmp, or change the image in the symbol editor to a transistor.
Once these changes can be made, a similar approach can be taken to the PcbNew and the Footprint Editor.
ON EDIT: The distinction created by the V6 icon background for Eeschema and PcbNew helps identify that one might be a subset of the other; but it just is not done well at the moment.
ON EDIT: The icon for PcbNew should include a relative white silkscreen layer in it; and also contain at least part of the footprint in the Footprint Editor icon.