When a habitat with many pokemon is wiped out to be replaced by a single species, that species is usually Man. This has happened before humanity; a couple million years ago, as a recent surprise find in Rusturf Tunnel has shown, Whismur are just as capable of driving out other life and making land their own. This is made even more remarkable by the fact that this was Whismur and not their evolved forms. The low height of this natural tunnel makes it a poor habitat for Loudred and Exploud; even today, Whismur are usually seen leaving the tunnel to evolve.
One can only surmise that, given the extremely loud noises Whismur even today are known for creating and the acoustics of the tunnel, which have the effect of dramatically amplifying sound, many of the native pokemon did not die so much as escape to protect their sense of hearing; indeed, many of the species the fossil record reveals in Rusturf do not show a single member with punctured eardrums.
Yet others, sadly, are far more numerous. Zubat in particular were extremely disoriented, for they rely on echolocation, and no Zubat can hear their sonar in a tunnel of screaming Whismur. This explains the numerous Zubat fossils with punctured ears, and perhaps the Whismur cave entirely, for it is difficult to imagine such small pokemon overcoming a cave full of Zubat in combat without deafening them first. The same applies to Geodude, the other numerous pokemon in the tunnel, who did not live long enough to go deaf; the extremely loud noise was enough to shatter their bodies instantly.
A loss of biodiversity is an admittedly terrible thing, but perhaps the Rusturf Tunnel of Whismur is preferable to another cave of rare pokemon interspersed between Zubat and Geodude.