Some of the differences in the movies:
-The opening sequences.
-Completely different soundtracks and composers for the entire duration of each movie.
-The Pokemon who appear as background characters.
-Dread's psychic-type partner (Reinculus or Gothitelle).
-Which Pokemon is Shiny (Janta's Golurk or Karita's Hydreigon)
-The left and right fork in the road.
-Cilan's macaroon basket is red in White, and blue in Black.
-Various scenes are mirrored.
-Ash does gymnastics when the basement cave begins to break apart in White, but merely runs for his life in Black.
-The battles between Reshiram and Zekrom are differently animated in each movie, using different attacks at different times in different ways.
-Same goes for the Pikachu versus Dread's psychic battles.
-Key plot point macaroons changed colors in each movie. For example, in Black, the macaroon Ash throws at the ocean is pink, and in White, it was white. - Serebii