Black is associated with death (in the West) and darkness. Red is associated with aggression (being a color that actual psychologically causes it) and bloodshed. Natural symbols of great destruction feature red and black, like forest fires and volcanic eruptions. Thus, Yveltal is red and black.
Alternatively, the colors green (representing life in the form of plants) and blue (representing life in the form of water, and also a psychologically calming color) are representative of life and creation. Forests, rivers, there you go, Xerneas.
As
>>17438842states, its inherently to evoke the Nazi banner and SS uniforms; the SS specifically designed their uniforms to be intimidating.
Most red flags are red to either remember bloodshed (the US and the Soviet Union) or demonstrate power (Nazi Germany). Most blue flags demonstrate peacefulness (the EU and United Nations).
Black flags are associated with pirates, and green technically with Islam (representing the fertile crescent).
