Some of the game's Pokédex entries seem to imply that the majority of prehistoric Pokémon become extinct due to their supposed "evolutions" hampering them in their natural environments, most notably Omastar's Red/Blue entry:
"A prehistoric Pokémon that died out when its heavy shell made it impossible to catch prey."
For the others:
Tirtouga and Carracosta might have been the ancient ancestors to Squirtle. Notably, Carracosta in particular has three finger-like plates on each flipper, the same amount of digits that Squirtle and it's evolutionary family have, Carracosta's toes are positioned in a similar fashion to Blastoise's, they both learn Rain Dance and Hydro Pump around the same level (Carracosta learning Hydro Pump one level after Blastoise and Rain Dance three), and the two have a negligible difference between weight average. The transition from Tirtouga to Squirtle might have been caused by the fact that Tirtouga's shell was extremely brittle and cumbersome, making the flexible, sturdy shell of the former more favorable for all practical purposes.
Shieldon has often been speculated to be the predecessor, or at least close ancestor to Aron. Compared to Aron, Shieldon not only had similar physical features, but it also had extremely similar abilities, including Metal Burst, a move that was exclusive to the duo and their evolutions prior to generation V. Shieldon and it's evolution were slow, could only strike hard when retaliating, and where vulnerable from their side quarters, making it seem logical that Aron's more evenly distributed metal plating be used in place of the lopsided "plate head" of Shieldon, which would also serve to balance out weight distribution across the Pokémon's body, giving it a mobility advantage.
Rampardos's demise would seem unlikely at first. Having sheer brute force that was surpassed at the time by only Groudon itself would seem to make nothing else matter, but as Pokédex entries state, constant trauma to the head cause the brute's brain to remain relatively small, allowing it to eventually be outsmarted by potential prey and causing Ramparados to die off slowly...And painfully. Come to think of it, Ramparados's general behavior and abilities are comparable to Ryhorn's along with having a bunch of spike-like proportions on the sides of its head, which might imply a relation of sorts between the two species.
Archeops and it's prevolution's decline can be explained by their ability. Potental prey merely had to strike their flimsy bodies in order to incapacitate them, and make a quick getaway.
Aerodactyl's disappearance is more enigmatic. Being both omnivorous and a formidable predator, starvation would not seem to be an issue for the king of the skies. Possibly, like the dinosaurs of real life, a cataclysmic event caused the demise of Aerodactyl along with other prehistorc Pokémon.
Groudon, while mostly notable for the Pokémon who clashed with Kyogre in a titanic battle, was implied to have at one point been an entire species rather then the single known living specimen seen today. These mighty creatures must have been the true masters of the prehistoric period, having power unmatched in all aspects, carving out individual mountains and volcanoes as their territory alone. As Groudon are apparently sterile, however, and only the violent processes present in the creation of the world produced the results necessary to bring them into existence, their population must have ever so slowly-but surely died down to the single, most powerful Groudon who was able to ensure it's survival for billions of years.
Tangrowth's entries stated that the vines which made up the bulk of it's body grew with such intensity that it couldn't see at points, making it impossible to catch prey, causing it to "devolve" into modern Tangella.
It should be noted that some fossil Pokémon, such as Kabuto, are not actually extinct, but have in fact been found in groupings while undergoing some form of stasis, meaning they could have been around for thousands, perhaps even millions of years, making Kabuto much closer to Relicanth in respect to other fossils.
