Rank 5: Climate Change

Even in the Pokémon world, climate change is a significant issue. The tundra Pokémon Amagarga likely lived during the ice age. A find of a perfectly preserved Amagarga encased in an iceberg made headlines.
The Pokémon has the ability to exude air at -150 °C. Such low temperatures on the surface of its skin indicate that the Pokémon does not cope well with heat. This may be a reason why it went extinct.
Rank 4: Bird Pokémon That Cannot Fly

Flapteryx (Gen 5) is considered the ancestor of bird Pokémon. It looks like a small bird modeled after an Archaeopteryx. However, although it is a Rock/Flying-type Pokémon and has wings, it has a significant weakness: it cannot fly.
Instead, Flapteryx hops from branch to branch or glides down from tall trees. This makes it hard for it to catch prey and it becomes a target itself. What was evolution thinking?
Rank 3: Overconsumption of Its Own Food

Lectragon and Pescragon come from the 8th game generation and, like Lecryodon, were formed from two fossils. Though the two Pokémon are quick enough to catch their own food, they seem never to have heard that catching prey must be balanced with the hunters.
The two Pokémon went extinct because they completely consumed their plant food and prey. Evolution was good to these two pocket monsters, but perhaps a bit too good. They were TOO skilled hunters and gatherers, which ultimately led to their extinction.
The saddest reasons for death can be found on page 4.