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It's due to a combination of artstyle, mechanics and clothes. If you took away all the stylistic touches (solid shading, massive veins and sinews etc) on say, Cyclomon, and then drew it sugi-style, no-one (who didn't know the digimon existed) would bat an eye as to its pokemonality. This also applies in reverse; Zekrom would make a great digimon if you mechanized it and added a few hatchmarks around the edges.
You've also got to take in to account the different scenarios that the series take place in. Pokemon ostensibly are living creatures living in a material world; animals eking out a living in a cruel reality, and thus most of them are supposed to look 'ecological', as in, seem like a creature that could have arisen naturally within the context of the franchise.
Digimon, in contrast, are computer-generated entities living in a computer-generated dimension. Nothing has to make sense there since it's basically just number-crunching.
...This does leave an open question as to where they get the mass from when they bio-emerge, but that's not the point here. The point is that within the context of the digital world, mons shifting from one form to another don't have to make physical sense as pokemon do.

There is also a more Doylist interpretation. Pokemon started out as a series of Game Boy games, where the goal was to capture and raise a variety of interesting superpowered creatures. The graphical prowess of the Game Boy allowed Creatures inc. to design large, informative sprites, but the physical limits on data space and sprite size meant that pokemon had to be designed to convey the necessary information while remaining legible. As the sprite area has increased over the years, subesquent  mons have been allowed to become more detailed, for refinement of the transferred information.

Digimon on the other hand started out as a series of virtual pets -- Tamagotchis for boys. They literally only had a 16x16 area in which to represent each digimon with nought but black pixels, such a limited space that it just wasn't worth simplifying the actual designs of each one to fit, so the artists could go all-out, as it were.