Many people think the new Black and White Pokemon characters look strange. But why is this? I think the reason is because the Pokemon company switched their design team. The biggest lost is the fact that Satoshi Tajiri has not worked on the games since the days of Gold and Silver. This is probably the main reason why Generation III and Generation IV Pokemon looked so different from Generation I and Generation II Pokemon. Generation V which is just coming out will probably look just as strange.
There is a team of people that are in charge of designing the monsters. They come up with all the ideas. They decide which ones are the best and refine them into the final characters. After that, Ken Sugimori draws the chosen designs. In the first generation, there was a group of four people including Ken Sugimore. Satoshi Tajiri, the creator of Pokemon, had the role of approving the monsters and suggesting changes after the basic ideas were designed.
Presently, Junichi Masuda took over after Ruby Sapphire. Ever since then, Satoshi Tajiri has not been working on the games at all. He's listed as the executive director in most games. What this means is that he is the original creator. He approved this game but was not an active part of its development. Sometimes he is listed as an executive producer, which means that he funded it but was not an active member in developing it.
So, to sum up, Satoshi Tajiri is not really putting an effort into the monster designs anymore. The Pokemon design "of D / P / Pt was held by thirteen people. Ten of these people did not work on the first generation's Pokemon. Shigeki Morimoto (he added Mew to the game) also stopped doing monster design during D / P / Pt . Therefor, the people coming up with the Pokemon ideas are, for the most part, different people each generation. R / S hired a lot of people, and that's why the third generation's style was so different. Black and White has also hired a different staff.
Look for some really different looking Pokemon in Generation V and beyond.