Why did Jesus favor Peter, James and John more than the other disciples? It's clear that Peter, James and John witnessed more miracles that Jesus did than the other disciples.  Why weren't the other disciples permitted to see the miracles that Jesus performed like Peter, James and John did?
You're making the mistake of an argument from silence, because in spite of your assertion that "its clear" that Peter, James, and John witnessed more of Jesus' miracles, all we really know for sure is that we have records that Peter, James, and John are reported to have witnessed more miracles than the other disciples. The fact that the other followers of Jesus are not mentioned in accounts of witnessing miracles of Jesus does not mean that they were not there, and all we can conclude for certain was that it was important to the writers of the various accounts to note that Peter, James, and John were witnesses, and that it was not so important to note that Thomas or James the Less also happened to be present. Before you can ask why the other disciples were not present, you first have to establish with certainty that you were not, and in the absence of any particular evidence in support of one possibility or the other, that is impossible to do. 

You should also remember that the very last verse of John's Gospel makes it clear that Jesus performed many deeds (which may or not have been miracles) which are not recorded. It is altogether possible that the other disciples witnessed more of these unrecorded deeds that Peter, James, and John did.