It could be flawed, but it could easily not be flawed, and there is a large body of evidence that in simplistic terms it is not. It could be that the large increase in the number of vaccines given at too young of an age is causing a large increase of problems. Not enough research has been done on that it seems. It could be that the way vaccines are manufactured has changed significantly and are more toxic now. It could be that vaccines are virtually ineffective and that child mortality decreases are solely due to improved hygienics as some claim, but the data I've seen by those that claim that is also flawed.
Whatever the argument is ones side is done a disservice if it does not correctly state the other sides position and adequately address it.