This is a tough one.
I think I'll put Dedenne at the overall top of my list. Not because it is a poor design (it is), or because it is competitively terrible (it is), but because it's not just unoriginal, it is the exact opposite of original.
Pikachu, being the franchise mascot and an overall cool cutemon from the first generation, turned out to be immensely popular. A small electric rodent with black, beady eyes, a squeaky cute cry and a happy and carefree behaviour. The kids loved it, and its name became just as famous as the term "Pokémon" itself.
So, when a new generations comes around, what does GameFreak do? Why, they make Pichu. It also became popular, featuring in a lot of media and sold loads of merchandise.
Naturally, they try to repeat the trick in the third generation. Plusle and Minun are generally well-received, if a little frowned upon because they look so much like Pichu.
Then Gen. IV and Pachirisu came around. The fans was beyond satisfied with the amount of cute, electric, suspiciously Pikachu-like rodents by now, but GameFreak decided to try to replicate the success yet again. It was generally seen as a poor attempt at emulating Pikachu, to try to sell more merchandise and plushies just as Pikachu and its successors had done so well.
Generation V, Emolga. A small electric rodent with black, beady eyes, a squeaky cute cry and a happy and carefree behaviour. Geez, when did we ever see that before? A secondary typing doesn't help it much. It's still widely regarded as a poor Pikachu clone. The fans responded largely with facepalms and frustration. "Okay, GameFreak, we've got it by now. Because there were two of them in Gen. III, we're actually ahead of schedule. Anyway, you've made enough of these now that we can fill an entire team with them. It's enough now, right? Right?"
Generation VI brought us many new takes on the Pokémon Lineup formula. The mandatory Metamorphosis Bug was given a spin by means of its design, essentially turning the GTS into a butterfly collection platform. The Early Route Bird was given a different typing than Normal. The Early Route Rodent was made somewhat uncommon, and its evolution inverted the concept of mandatory cuteness. The Legendary Trio was scrapped outright. But what about the Pikaclone? Having seen all this norm-breaking and variation, one would think that they had reconsidered the concept of Pikachu emulation too. But what did we get? A small electric rodent with black, beady eyes, a squeaky cute cry and a happy and carefree behaviour. Okay, it has a secondary Fairy typing, but its design doesn't reflect on this in any way. It's a lazy Pikachu clone without any distinguishing features. Another plushie-selling, Anime-spotlight-grabbing piece of cuteness trying to ride on the back of Pikachu's popularity. Included in the Gen. VI lineup just to fulfill that role. Not designed because of creative spirit or to be original. It had a very strict set of design specifications, and a role it was set to fulfill even before it was clear what it was going to look like, or what its special abilities were. A strict reminder of how commercial Pokémon really is. They're breaking the fourth wall with these Pikaclones, telling the viewers/players that since they liked the concept so well the first time, and paid lots of money to show their appreciation, they're going to get it again and again and again for as long as the franchise stays alive.
Other than that, Vanillish/Vanilluxe get honorable mentions for their ridiculousness. I would have liked them if they were designed to be icicles somewhat resembling ice cream cones, but instead they were created to be ice cream cones somewhat resembling icicles. A little too man-made-looking and derpy for my liking.
Barbaracle is just ugly and deserves to be featured on this list.
Garbodor, a frequent customer of lists like this, is a victim of poor graphics and a terrible choice of pose in all its appearances. If interpreted as being a terribly filthy, toxic creature living among garbage instead of being actual garbage come to life, it is actually quite a cool concept. A shame that GameFreak chose to display it as a derpy heap of silliness rather than a poisonous ogre scavenging landfills for food, using its smell and toxicity as a means of defense.
