It probably had something to do with buying the rights to the characters. There are a LOT of characters in the Mario universe, and if DiC(the maker of the cartoons) made all the characters look EXACTLY like they are in the video games, they'd have to buy the rights from Nintendo. Lets take the Koopa Kids for instance. The Koopalings belong to Nintendo, so DiC has to buy them from Nintendo. But, by changing the Koopa Kids' appearances slightly and changing their names, they don't have to pay Nintendo(well, not as much, at least). The same applies to many of the other characters as well. If they left each and every character EXACTLY the same, they'd have to pay Nintendo a WHOLE lotta money. (And DiC sucks, so they didn't really have much money in the first place)
However, this isn't the case for all of the characters. Some characters look different because of the way they were in the old NES games. Take Princess Toadstool for example. If you look at her in the original SMB2(US), she has red hair. King Koopa looks similar to the way Bowser looked in the original SMB. However, he also vaguely resembles Wart. Since he used a lot of Wart's minions in the cartoon, my conclusion is that the animators were trying to combine Bowser and Wart. Either that or they were just too lazy to draw the real Bowser. (Knowing DiC, it was probably the latter =)
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