But the vast majority of those mutations are either deleterious or "neutral" and proving even a single beneficial one that could be passed on is rare and often not even a certain thing.
Why would it need to be any more than rare in order to produce the biodiveristy that we see today?
No, you observe new phenotypes emerging but the idea that this is due to mutations is purely theory.
It is no longer a theory, as is shown in rock pocket mice.
Just a moment...
The new phenotypes emerge due to the shuffling of the allele frequencies brought about by the reproductive isolation alone working on the BUILT-IN alleles shared within the new populations.
Evidence please. In the case of the rock pocket mice, the dark allele is not found in the rest of the population, and it is not due to a combination of the existing light fur alleles. You are clearly wrong.
BUT EVEN IF MUTATIONS WERE THE SOURCE OF THE NEW PHENOTYPES, you still have to have a reduction, sometimes elimination, of the competing alleles for the traits that emerge in the new population.
If that mutation only happens in one population, and is selected for, what you have is two populations with different alleles, and different alleles than were found in their ancestors. That is an increase in genetic variation by every measure.