For much of the Pokémon franchise's long history, its titular monsters were depicted mostly in 2D, whether in the anime series or video games. In the video games' relatively recent transition to 3D designs, certain Pokémon's 3D models lost much of the flair of their 2D sprites, leading to several that look goofy or just plain bad.
Granted, fans had already seen 3D Pokémon before the Nintendo 3DS' Pokémon X and Y. The N64's Pokémon Colosseum and other console titles included blocky polygonal versions of various monsters, for example. But the rudimentary nature of many of these depictions made any design oddities understandable. The same can't be said for Pokémon's more modern 3D entries.
Since X and Y, the main Pokémon game series has worked with 3D models of a much higher fidelity. In many cases, these models adequately mimic the Pokémon's original sprites and/or official artwork, but a few creatures changed for the worse. Here are a few Pokémon whose 3D models look uglier than their 2D sprites (and the official 2D artwork based on them).
Pokémon That Look Worse With 3D Graphics: Stunfisk
Many of the worst-looking 3D Pokémon designs qualify as such because their 3D models, ironically, show less dimension than their sprites. Stunfisk demonstrates this at its most literal. In 2D, players could see its face and body, but it's reduced to a flat line on the horizon in 3D. This is almost certainly part of the joke: Stunfisk is meant to be a goofy, dumb Pokémon, and its true flounder-ization in 3D only enhances that goofiness. That doesn't change the fact that it looks bad - arguably worse than its 2D design.
Pokémon That Look Worse With 3D Graphics: Tropius
Several Pokémon that dwelled on the ground in their original designs were made to awkwardly hover in the air in 3D, but Tropius is without a doubt the oddest. It went from a towering, tree-like dinosaur, roaring as it turned to face its opponent, to a goofy, hovering Loch Ness Monster that begs fans to ask how it can possibly fly. Its rear view looks even worse (see Bulbapedia), as it exposes a plain, smooth backside.
Pokémon That Look Worse With 3D Graphics: Marshtomp
As was the case with Tropius (and will be the case with the next two entries in this list), part of what makes many 3D Pokémon look odd is their lack of a defined expression, mostly due to newly closed mouths. Few Pokémon fans would likely argue Marshtomp was ever a high point of good Pokémon design, but it at least had a charming smile. Its 3D model's weirdly just-barely-open mouth trades its happiness for discomforting contentment, and its perfectly symmetrical features make it look creepily stiff compared to its 2D design.
Pokémon That Look Worse With 3D Graphics: Typhlosion
The transition to 3D made one of Pokémon's coolest Starters into a lame weasel. Typhlosion's 2D sprite caught it in the middle of a fire-spewing snarl, but its 3D model cut the flames (which now appear only during certain animations) and left it in a sort of disinterested pose. Typlosion's entire identity comes from those flames and that face, so removing both left it a shell of its former self.
Pokémon That Look Worse With 3D Graphics: Hippowdon
Perhaps the worst-translated Pokémon to 3D is Hippowdon. Its original sprite was one of the most intimidating of its generation, with sand spewing from its side-holes, a gigantic mouth barred at its enemies, and a pose that suggested it had just risen from the ground in a surprise attack. In 3D, it's just a bored-looking hippo, standing there on its terrible, terrible teeth-feet. Like Typlosion, the removal of its elemental accessories makes sense, situationally and anatomically, but it makes for an overall worse Pokémon design.