Togepi has tan skin, but its evolutions are white all over. Why the change? Togepi is a baby bird, its feathers grow in when it evolves!
Regular Ampharos is primarily yellow, with a red orb on its tail that emits light and the Pokemon itself is often used in lighthouses to guide ships. Shiny Ampharos is pink, with a blue orb on its tail. Lighthouses sometimes alternate using red and white (or blue) light to guide ships; and as for the body color, there's an old rhyme that goes "Pink in the morning, sailor's warning; pink at night, sailor's delight".
Why does Sudowoodo disguise itself as a tree? If you think about type weaknesses and resistances, it makes sense for a Rock type to disguise itself to look like a plant (and thus trick people who don't know what it is into thinking it's a Grass type). This is because if it gets into a battle, an opponent who thinks it's a Grass type would hesitate to use Water, Ground, and Grass moves against it, which are types that Grass type Pokémon resist but Rock types are weak to. Conversely, someone who thought it was a Grass type would probably use Fire and Flying moves against it, which Grass types are weak to, but Rock types resist. Also, while Bug and Ice type moves are neutral to Rock, Rock type moves are strong against those Pokemon. So by pretending to be a Grass type, Sudowoodo can trick unsuspecting trainers into using less effective moves against it, while avoiding moves of types it would be weak to.
Miltank is now regarded as a female version of Tauros, yet she can't produce Tauros eggs. While this doesn't make sense from a biological standpoint, it does make sense from a gameplay standpoint breeding two Pokemon always yields offspring taking after the mother.
Delibird has the ability Vital Spirit, which prevents sleep. It would need this because it's based on Santa Claus, who delivers presents all night.
Lugia used to reside on the top of one of two towers in Ecruteak City, though it now lives deep in the Whirl Islands. It is known to have the power to both calm and give rise to storms. Several Pokédex entries mention that Lugia isolates itself because its powers are too strong. Now, back to the two towers in Ecruteak. One of them is still standing; the other one burned down when it was suddenly struck by lightning. Guess which one Lugia used to roost on?
The Pokémon that died in the fire in the Tower were probably Flareon, Vaporeon, and Jolteon, but came back as Entei, Suicune, and Raikou due to Ho-Oh's powers.
This is backed up by the Beast Trio's Dream World abilities being the same abilities said Eeveelutions possess normally!
Sadly no longer the case as of Gen VII, which switched the Hidden Abilities of all three to Inner Focus for some reason.
AND the fact that three of the Kimono girls use Vaporeon, Jolteon, and Flareon. Perhaps these three gained some sort of worship status?
Remoraid evolving into Octillery is pretty weird as a remora turns into an octopus, but it makes more sense with their secondary themes: a hand-held pistol and an artillery cannon.
There is also a biology theme tied to Remoraid and Octillery, and its theme is actually suckers. With octopi, it should be obvious with their suction cup tentacles, but remoras, one of Remoraid's inspirations, can attach itself to other larger fish with its frontal fin acting like a suction cup. In fact, it can be seen in pre-Gen IV Mantine's sprites doing exactly that.
It's mentioned in multiple Pokédex entries that there's a secret about Wobuffet's tail, which they are oddly protective of and try to hide. But why does Wobbuffet look and act like an inflatable punching bag, even in the Super Smash Bros. games? Because that's exactly what it is — the black tail is the actual Pokémon; the blue body is merely a protective decoy. That's why it has eyes on its "tail", but closed eyes on the "body"; the latter are fake "eyes" to make it look like a face, misleading opponents into thinking that they're looking at its front and its actual head is just its tail. It also explains why the "body" can take hits but cannot attack on its own.
A common occurence in many Gen II evolutionary lines is wildly different colors between stages the Hoppip line goes from green, to pink, to blue; Remoraid goes from blue to red, etc. A player that started with later generations would think this would make the lines less cohesive. But back in the day, it was a good way to show off the games new color screen.