Hopefully linking to another site is fine, please don't take it as a personal attack towards the site. With that said...
https://gamefaqs.gamespot.com/top10/3076-the-top-10-overused-and-underused-pokemon-inspirations
This list starts pretty good but not perfect, listing many things GameFreak likes overdoing and things they don't use as much. It's fairly interesting and worth reading.
Then comes #1 and the list does a 180º turnaround, complaining about the most unique and creative Pokémon and asking for generic fantasy creatures every fantasy series has. What? Seriously, why are object Pokémon a bad thing? Who said Pokémon must be based on living creatures only? That's ridiculous. Especially when he proposes having a pegasus named Pegasus. Boy sure that's original and interesting! The Litwick family shows far more imagination and clever design than any boring horsebird ever could.
But hey, who cares about that when you can milk the overused Trubbish mockery for cheap laughs?
Let's go through this one by one:
#10: OVERUSED: MICE AND RATS; UNDERUSED: BUNNIES, GERBILS, AND GUINEA PIGS
Right of the bat I feel we're splitting hairs. From what I read, it's not exactly mice and rats they think there too many of but rather it's the pikaclones. They're tired each gen has an electric rodent of some kind. Well, TOO BAD. Pikachu is the series mascot and thus each gen gets its own pikaclone. But to confound the error even more by stating bunnies, gerbils, and guinea pigs aren't represented. Well, sorta, they do point out there's Bunnelby and Buneary for bunnies... and consider ALL THE OTHER SPECIES OF ANIMALS that HAVEN'T been made into a Pokemon, I would say bunnies getting two families is pretty generous and if anything we DON'T need any more unless based on a specific notable breed of rabbit/hare. Also, I like how they make fun of Dedenne then says there's no gerbil Pokemon... DEDENNE IS A GERBIL! Which also sort of relates it to the guinea pig! And they call Minccino rat-like... when it's clearly based on a chinchilla. In addition, not all Pikaclones are rodents, Togedemaru is a hedgehog! We're not past the first category and already the writer doesn't know what they're talking about.
#9: OVERUSED: GENERIC FISH; UNDERUSED: DOLPHINS, SHARKS, AND WHALES
Okay, something a bit more understandable. We do has a slew of fish Pokemon and not all of them are that interesting (though to be fair there's thousands of species of fish a Pokemon can be based on, many with interesting traits. They can be made interesting much like the bird Pokemon the writer allowed to slip for they had some interesting bird species made into Pokemon (though also just as many generic, if not having more generic birds than fish)). I can also understand how Sharpedo and the Wailmer family may not really satisfy those looking for a shark and whale Pokemon. And we've been wanting to see a dolphin Pokemon since they started introducing new Pokemon.
#8: OVERUSED: HUMANOIDS; UNDERUSED: KANGAROOS
I kind of feel they're stretching here. This list sounds really like the writer's wishlist than actually complaining there's too many of a specific kind of Pokemon structure. Like here, they wanted to say they wanted a more Kangaroo Pokemon than Kangaskhan. Fine, okay, but in order to work in their format the "overused" category is humanoid? A weak connection, especially since humanoid is such a WIDE category with plenty of design opportunities. Oh, and not to mention that Human-Shape is a Breeding Category so there's justifcation for all those humanoid looking Pokemon (aside giving the designers an opportunity to make an interesting Pokemon)! And yes, it's weird the humanoid Pokemon have what looks to be clothing but would you rather them be naked or suspend your disbelief that they just so happen to have natural body coverings that resemble clothing. We have neon yellow mice that can shoot electricity, Pokemon wearing clothing is far from the most extreme thing you have to overlook.
#7: OVERUSED: SEALS; UNDERUSED: PLATYPI
Well at least they're both sea creatures (though personally I think a Platypus would make for a good Electric/Poison). No problem here really, and honestly he's right that we don't really need another seal-like Pokemon because we sorta got the three common ones: dugong, walrus, and sea lion. And platypus is up there with dolphin for wanted Pokemon.
#6: OVERUSED: DOGS AND CATS; UNDERUSED: WILDCATS
... What is this writer going on about? Okay, yes, we have a lot of normal household cats but it's not like we don't have wildcats. Pyroar, Luxray, Liepard, Raikou is more sabertooth tiger than a canine which you shoved all the Legendary Beasts under. Each generation they introduce new canine and feline breeds, both a mixture of household and wild. Also, not to mention a lot of the wild cats and dogs you mention have similar features to one another so why are you asking them to have separate Pokemon based on similar animals (if they aren't already a Pokemon, some of whom show traits of multiple similar canines or felines like Liepard)?
#5: OVERUSED: FOXES; UNDERUSED: MOOSE
I'll give you this one. Due to how popular the mythical Kitsune is it has allowed a lot of foxes to be made. We can probably start focusing on other animals, like a moose. I'm good for a region based on Canada. Also the fact they don't know what is Keldeo is a major clue they done NO research (even if you don't know its based on the mythical kelpie it still looks like a pony! Does it need a cutie mark to clue you in on that?). Also I want to quote this:
I'm holding out hope that one of the starters in Generation 8 could be moose-based. A moose-based grass type, a dolphin-based water type, and a giraffe-based fire type could render this entire list outdated in one quick swoop.
... What's the point of this list? Because, yes, Gen 8 could very well easily make this entire list irrelevant and very possibly will. Now the moose, dolphin, and giraffe may not be Starters, but they can still have normal Pokemon be based on them. And each generation does have GF introducing Pokemon based on new animals and mythological creatures (though ones you may not be familiar with but we'll get to that). If you wanted to wishlist, make a wishlist. Don't start saying "there's too many of this kind of Pokemon" just because ones on your wishlist haven't been done yet, especially when you're not even going to do any research.
#4: OVERUSED: TYRANNOSAURUS REX & BRONTOSAURUS; UNDERUSED: MOST OTHER DINOSAURS
Okay, I see your point that the theropod and sauropod body type is overused even if the Pokemon isn't technically a Fossil Pokemon. And I agree that would be neat to see the other dinosaurs too like stegosaurus and ankylosaurus. That said, we do have Pokemon based on other dinos as you noted. Also, dinos aren't the only prehistoric creatures and just focusing on dinos alone closes the door to other equally as neat possibilities. I'll give this point to the writer, though expand "most other dinosaurs" to "most other prehistoric animals".
#3: OVERUSED: FLOWERS; UNDERUSED: TREES
From what I see there's just as many flower Pokemon as there are tree Pokemon. Also venus flytraps and pitcher plants aren't flowers. And Trevenant is an ent (a copyrighted name, BTW)! "How many ways can you make a flower fight"? I don't know, how many ways can you make a tree fight? Look, I'm glad you found a batch of interesting tree species you think deserve attention and maybe be made into a Pokemon, but you aren't seeing the forest for the trees.
#2: OVERUSED: MONKEYS; UNDERUSED: GIRAFFES
Now at first I was going to give you this point, but then I realized I shouldn't. Why? Because there are many kinds of monkeys/apes and generally only one kind of giraffe, maybe two if you count the Okapi. Of course there's going to be a batch of monkeys/apes! Should there be a giraffe (aside from Girafarig which is its own complexity)? Sure. But to say monkeys/apes is overused is like saying they used too many bird Pokemon but don't have a flying lizard, you're comparing an entire genus of many species to a single species.
#1: OVERUSED: INANIMATE OBJECTS; UNDERUSED: MYTHICAL CREATURES
Wait, let me correct that:
#1: OVERUSED: INANIMATE OBJECTS; UNDERUSED: MYTHICAL ROMAN/GREEK CREATURES
Because that what the writer means. Because they can't be asked to do research to discover a LOT of Pokemon are based on mythical creatures from other countries (notably Japan's Yokai because, well, Japanese games). I'd say even more are based on mythical creatures than objects... heck, the objects themselves are based on a Yokai. However a clue what they really mean is when they list the mythical creatures they're thinking of: mostly Roman/Greek ones (with Bigfoot thrown in and... Tanuki? What, does Zigzagoon need a giant pair of balls to clue you in?). Now, while it would be awesome to see Roman/Greek mythical creatures made into Pokemon, to say mythical creatures overall are underused is just naive.
Writer, if you're going to present a poorly researched article, just skip the pretense and make a plain ol' wishlist like the rest of the internet. Sure, you may be ignored, but at least you won't look like you have no idea what you're talking about because you didn't want to spend an afternoon on Bulbapedia. My "
Not Yet A Pokemon Repository" looks more researched than this article and it's just a giant list of animals, objects, concepts, and mythical creatures!