Although there have been more fossils found than they know what to do with, there have been no intermediate fossils found.
Even today with resistant bacteria, scientist just find it. They don't know if they just appeared or it took generations of bacteria.
If penicillin resistant bacteria came from normal bacteria then wouldn't normal bacterial have to experience penicillin to become resistant? Yet if penicillin kills bacteria there would be no offspring to improve and make the adjustment and no mutational events can happen.
The Origin of the Species isn't the about the origin at all. It picks things up in midstream.
If man did evolve from apes then why is the ape sill around. Wouldn't natural selection discard the ape if man was better?
If fish evolved into amphibians, then into land mammals, how did fish know land would be a better habitat when they have never experienced it? Again wouldn't natural selection discard the fish?
The theory works much better within each species to explain some aspects of survival.
Like many theories there are too many questions that defy reality and common sense.