There's a
team of people that is in charge of monster design. They're listed under "Pokemon Design." They come up with the ideas. They decide which ones are the best and refine them. Then, Ken Sugimori draws those designs. In the first generation, it was a group of four people (Sugimori being one of them), and Satoshi Tajiri's role (the creator of Pokemon) in creating the monsters was basically to approve them and suggest changes after the basic ideas were being designed. He's the only one under "Director" and "Game Design" for the first generation which means that he was in charge of pulling everything together and the overall experience of playing the game.
Nowadays... well, the truth is that in
Ruby and
Sapphire, Junichi Masuda took over. Ever since R/S/E, Satoshi Tajiri has not been working on the games at all. He's listed as "Executive Director" in most games. What does this mean? "Executive Director" is a fancy way of saying "this is the original creator, he approved this game but was not an active part of development." Occasionally he's listed as an "Executive Producer," which, from what I can gather, means he funded it but was still not an active member in developing it. Finally, in
Pokemon Rumble (surprisingly enough), only Sugimori and Masuda are listed in the credits as "advisers" for the spin-off game. Tajiri is not listed at all.
So, Satoshi Tajiri is not really putting his mind into the monsters anymore. However, there is another part of why the monsters look different. 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's the guy who put Mew into the game) also stopped doing monster design during D/P/Pt. What does this mean? The people coming up with the Pokemon ideas are, mostly, different people each generation. R/S hired a ton of people, and that's why the third generation's style was so different.
Black and
White has also hired more people.
Thus, the main reason why the
Black and
White Pokemon look weird is because the design team has new people on it. Also, Satoshi Tajiri hasn't worked on the games for a looooong time (since the
Gold and
Silver days), thus the reason why Gen III and Gen IV looked so different from Gen I and Gen II. And now Gen V could look very different as well.
