I think not only Zekron and Reshiram manifested the opposite something. Even the version-exclusive pokemon are opposites. Reuniclus and Gothitelle are examples: Simply by the look of Reuniclus, we can see that he is a happy guy, whereas Gothitelle is not. And Reuniclus somwhat means a "union" of something. Gothitelle on the other hand is an allegory to a separation from reality and society.
Braviary and Mandibuzz is also an example. Braviary is a war-eagle. It shows vitality. Life. Mandibuzz on the other hand is the Pokemonification of death. Sorrow. Sickness.
Alder is also an opposite on his own. Between want and need. As from what I understood, Alder wants to travel the whole region again. However, due to his post, he needs to go back to wherever he is (the League) to fulfill his duty.
Yes, they really show this feature well.
Bianca and Cheren sort of also showcase opposites.
It's even evidenced in their names.
Bianca = Italian for "white"
Cheren = Hungarian for "black"
and of course Hilbert and Hilda have opposites too:
Their Badge Cases are different colors (Hilbert's is blue and Hilda's is pink).
Also, the pencil in the saving animation is different color depending on Hilbert or Hilda as the player.
Hilbert has black on his hat (he was once known as "Black") while Hilda has white on her hat (she was once known as "White").
And before the official English names were revealed, they were referred to as "Blair and Whitlea" and "Kuro and Shiro". Both mean Black and White.
Hilbert and Hilda are also opposite in some way.
It's not just with Pokemon I see opposites, but the main human characters too.