I dunno, gen 1 had some pretty [parasitic bomb] pokemon too. There were so many that were just larger versions of real world animals with changed colours. And then, y'know, Grimer. It's an animate puddle. It evolves into a bigger animate puddle. Voltorb. It's a ball that shoots lightning (?). It evolves into a bigger ball that shoots lightning. Hitmonchan. It's a boxer? And Magnemite and Diglett, while having nothing wrong with them themselves, have the laziest evolutions ever. Those two look especially bad compared to Metagross, who actually did the whole combining pokemon thing right.
There are plenty of badly designed pokemon in the later gens, but there are just as many good ones as in the early games. Breloom and Ninjask and Flygon and Milotic and Dusknoir and so on and so on and so on.
Metagross is the best pokemon ever so I'm going to keep complaining at you until you acknowledge it so just do it already. :<
Hold on, now I've got to comment on a whole list!
Gen 1: Again, designs that blend in WELL with inanimate objects are fine. Bronzong looks like a bell melted on a totem pole (which are WOODEN). Magmar, Jynx, and Electabuzz are my only real Gen 1 complaints.
Breloom: Cute, but not practical. Mushrooms do not have tails, or that much green.
Ninjask: Good blend of theme and imitation of the animal. Excellent.
Flygon: There are better ways to do what looks like a dragonfly. Yanma.
Milotic: Played more as an eel instead of a dragon, it might have been okay.
Dusknoir: With ghosts, it's just too hard to say "Well this is too abstract." So it's lucky.
Again, all is a strong word. Metagross isn't too terribly bad, especially if one considers Steelix and Magnetron acceptable.
And Houndoom's my personal favorite, but objectively, I'm not sure what the best design is. Most would probably say Pikachu considering how darn universal his appeal is.