"What are the two are three biggest weaknesses of the modern evolutionary synthesis?"
I don't think there are any serious weaknesses. If there were, evolution would not be a scientific theory.
There are areas where more information is desireable, like the Precambrian fossil record. But it is unlikely that a huge amount of fossils will be discovered from that period, in any event.
I don't think that's true. Punctuated equilibrium is a scientific theory, but mainstream evolutionists seem to identify substantial weaknesses in it.
Don't you agree?