Alright, I think I see what you're asking.
BW/BW2 apply three-dimensional aspects to the game in the sense of how certain over-world locations appear, most notably the streets of Castelia City. In fact I remember being smitten over the graphics when the game came out, ah nostalgia. These were the first games with fully animated sprites, the developers were certainly taking advantage of their ability to advance the graphics of the game and make a more immersive gaming experience.
With all of this and the modern 3DS Pokemon games we have now, it makes sense that you could think the game was intended to be 3D like Pokemon XY was.
However, despite the fact that the graphics are advanced, it is in its entirety a 2D game. What you're seeing are 2D images placed in a way that give of the impression of it being in 3D, which is a basic artistic tactic. In terms of how we understand "3D" to be now, when referring to the games on the 3DS that actually appear to pop out thanks to the utilization of two screens overlapping each-other; then the answer is no, BW/BW2 are not actually 3D games.