Everything here are completely based off of my observations and is not in any way an official or consolidated list, so if you notice any design inconsistencies yourself, whether it be from a completely different Pokemon or just an additional variation to the Pokemon already on here, I would love it if you contacted me about them!
The skin color of Jynx's original design was the subject of alleged racism and controversy, so she had to be changed to a different color.
|Image of Jynx from the original anime and Jynx's old RBY sprites
Jynx's face and arms used to be black.
|Jyn'x Sugimori Art
...Until a hasty change by Nintendo which changed her skin color to purple.
Pay attention to Arbok's "face" markings on the underside of its hood. There are currently three variations of these markings, although Arbok's Yellow Pokedex flavour text says that there are six.
|Image from an anime episode of Arbok
Arbok's current standard design.
|Dark Arbok card from the Team Rocket Set
Notice the bared teeth on the "mouth" marking and the redesigned, inverted colors on the "eye" markings, and the absence of "eyebrows" (that black stripe above the eyes in the standard design). This Arbok design is an anomaly and seems to have been altered just to suit this specific card's design and doesn't reoccur again.
|Arbok card from the Fossil Set
This set of markings is the major deviation from the standard design. The "mouth" now has its tongue out and the "eyes" have pupils.
|Janine's Arbok card (Japanese only)
A Japanese card of Arbok with the same design as the one above.
|Arbok's Gold and Ruby/Sapphire Game Sprites
The deviation of the standard markings, with the pupils and the tongue, seems to have actually been the standard design for the second and most of the third generation sprites, as the Gold/Silver/Crystal sprites and the Ruby/Sapphire/Emerald sprites bare this design.
|Arbok's Red/Blue and Diamond/Pearl Game Sprites
With these sprites we can see that Arbok actually started out with the standard design we have today (the markings with no pupils and a completely black mouth) as the Red/Blue version of the sprite indicates and has, since the fourth version, reverted back to this design and decided to stick with it, as the most recent generations, Diamond/Pearl and Black/White, have these markings. What's particularly interesting is that the FireRed/LeafGreen sprite also has the standard marking, while the rest of the third generation games have the other secondary design. This suggests that maybe the Kanto region contains only the standard Arboks, as Arbok's flavour text cites that the markings change depending on the area that he is in.
The number of gold horizontal rings on Ekans' body has changed over time.
|Ekans' Modern Sugimori art
His standard design currently has only one golden ring, the one around his neck. There are horizontal lines running across his body to signify further segments on his body, but these are still purple and more or less blend right in with everything else.
|Ekans card from the Team Rocket set
This Ekans design has all the minor segments colored in gold, and we can see from this card (the art is also from the old Sugimori images, by the way) that he has at least four golden rings rather than just the one around his neck. This design doesn't show up anywhere else as far as I know.
Horsea's back fin has changed around quite a bit.
|Horsea's Sugimori Art
This is Horsea's standard design. Pay attention to the size of his fin since it seems to be subject to a lot of size changes.
|Old Sugimori Art of Horsea
This is the only image we see of Horsea with two back fins, not one.
|Horsea Card from the EX Dragon Set
Horsea's back fin has reached epic proportions in this card.
|Horsea's Diamond/Pearl Back Sprite
His back fin is pretty sizable in this back sprite too, but not as much in the other TCG card. Still way bigger than the standard design, though.
|Horsea's Gold/Silver, Black/White, and Ruby/Sapphire Back Sprite
Despite a random deviation in back-fin size in the third generation, Horsea's fin size has pretty much stuck to its standard size throughout the sprite generations. The first generation back sprite of Horsea is way too pixely made to make out much.
The shape of the part of Blastoise's shell that cover his water cannons are either round or square, and how much the cannons protrude from his back.
|Blastoise Anime Screenshot and Blastoise's Sugimori Art
Here we can see that Blastoise's water cannons are enclosed by his shell and are a square shape (I circled the part in red just in case it's not very clear what I'm talking about). This seems to be his standard design in the anime but not so with his game sprites.
|Old Sugimori Art of Blastoise
Blastoise's shell on top of his water cannons are clearly rounded and do not cover the sides of the cannon as in the standard design. Instead, the sides of the cannon are left exposed with only the top covered.
|Blastoise's Gold, Green, Silver, and FireRed/LeafGreen version game sprite
The shell design in these sprites are extremely similar to that of the old Sugimori art above: rounded and not completely covering the canons up. The Silver and FireRed/LeafGreen sprite especially has his cannons protruding way out from his back.
|Blastoise's Diamond/Pearl Sprite
Only since the fourth generation that the game sprites have displayed Blastoise with his standard design, with the enclosed and square-shaped shell.
Other than one anomaly with Cloyster's shell, his design has remained more or less consistent.
|Cloyster's Sugimori Art
Cloyster's standard design.
|Cloyster's Red/Blue Version Game Sprite
For some reason, his Red/Blue sprite has his shell flipped the other way, so instead of the crack being on the top, it's on the sides now. All other images of Cloyster, in the anime, TCG, and all other game sprites, have his shell the right way around.
Exeggutor is an interesting case because he was not subject to any direct design changes, but rather it seemed Nintendo never really figured out what to do with a back-shot of him until the fourth generation. I think it's quite apparent that Exeggutor was always supposed to have three heads only, since almost official images of Exeggutor show just the three. However, the number of heads and how much the coconuts covered up his body, whether they were only in the front or from all sides, was never really settled until the fourth generation.
|Exeggutor Sugimori Art
Standard design of Exeggutor, featuring 3 heads and maybe more.
|Screenshot from the March of the Exeggutor Anime Espidoe
Obviously this episode featuring Exeggutor put 4Kids in quite a tight spot because we never were really shown the true back of Exeggutor, unless you think that Exeggutor's coconuts/heads surround his body all 360 degrees. In this screenshot we can clearly see that 4Kids tried really hard to draw only 3 heads on each Exeggutor, although you can see parts of a fourth head.
|Another Anime Screenshot
Here we can clearly see five heads in total.
|Back Sprites, Generations 1-3
Just an illustration of Exeggutor's ever-present heads covering up his entire body all the way around.
|Exeggutor's Black/White Back Sprite
And finally, in the fourth generation, we finally get to see some section of Exeggutor that isn't totally covered up by a coconut, the part where the leaves directly meet the trunk! Looks awkward, but I'm glad the designers finally resolved this issue and settled on three heads, which I will assume will become the standard design for Exeggutor.
Venomoth's design has only changed in one instance.
|Venomoth's Sugimori Art and Black/White and Gold/Silver Back Sprites
Venomoth's standard design. Notice especially the design on the back of its wings and how they are the same as the ones on the front.
|Sabrina's Venomoth Card
The back of Venomoth's wings, rather than being the same design as the front of his wings, instead display a different one, featuring a row of yellow circles. This is the only image in which the back of Venomoth's wings have this design.
Vaporeon's tail seems to have gone through one or two variations.
|Vaporeon's Diamond/Pearl, Silver, and Ruby/Sapphire game sprite, respecitvely
Vaporeon's standard design, which has remained more or less consistent throughout the ages.
|Vaporeon card from the Jungle Set
Here, as opposed to the standard design, we can see that Vaporeon's tail, rather than being fleshy and consistent with the rest of his skin, is filmy and thin, similar to an actual fish's tail. It's a shame that this design didn't stick because I actually think Vaporeon looks a lot better like this.
|Vaporeon's Yellow Version Sprite
Although the sprite is not clear, the disconnect of the whiteness of Vaporeon's tail as oppposed to the rest of his light blue body suggest that he has a thin, filmy tail similar to the one above. Vaporeon's Red/Blue sprite show the fleshy tail of Vaporeon's standard design, though, so it's hard to say what the creators of this sprite were intending his tail to be like.
Mostly some subtle coloring inconsistencies near the tips of his wings.
Farfetch'd's Red/Blue and Green Sprites
Here two clearly defined lighter stripes are present on his wings.
Farfetch'd's Gold and Silver Sprites
Moving on to the next generation of sprites, the two light stripes have merged into one really big and thick stripe near the end of his wings. Although it's impossible to tell in all of Farfetch'd third generation front sprites, his back sprite from the Ruby/Sapphire generation clearly shows this same light stripe.
Farfetch'd's old anime art, Black/White back sprite, and Platinum sprite
And here the stripe is gone and his wing is just a consistent brown color. It's interesting to note that his old anime art and an old anime episode featuring Farfetch'd are just as old as the Red/Blue sprites, so this means that the brighter stripe on his wings only appeared on his game sprites.
His blowholes miraculous disappeared in the 5th generation.
Wailmer's Front/Back 4th Generation Sprites
Notice the two, clearly defined blowholes above his eyes. They were present in the 3rd generation at his conception as well.
Wailmer's Black/White Sprites
And then all of a sudden the blowholes are nowhere to be seen.