I held a rock of 3.6 Ga (Giga Annum= 1 billion (sp?) years) in my hands today, so definitally Rock Pokemon like Geodude and co.
Also Fire/Ground Pokemon that could live in the harsh conditions of extreme Heat.
During the "Snowball Earth" (considering the Pokémon world had the same history as our planet) there would be an abundance of Ice Pokemon (Swinub, Piloswine and Mammoswine (probably less "evolved", since Mammals came late), Glalie, Snorunt).
During Cretacious, Jura, Trias, Dinosaur-like Pokémon such as Tropius, Torterra, Charizard, Aerodactyl, Gligar... Later small mammals such as Rattata, Raticate, Pikachu...
When the earth was recovering from the Meteor strike 65Ma (Mega Annum=1 Million years) ago, there would be Pokémon who could live in conditions that don't ask for much light. Diglet, Dugtrio... Sandshrew.
During the Devonian/Carbon Era, major insects, like Yanma and Yanmega. Since it is the Era of the woods, I might add Sudowoodo as well. x3 Exeggcute/or.
I did have a course about the Origin and Evolution of Life today... 8D Yey for Paleontology.