Also, when Neo meets the Architect and all his predecessors are displayed on screens, the current Neo is the only one that is not surprised to hear the Architect say "that was quicker than the others", all the other versions of Neo lose the plot.
And if every version was quicker than the last leading to an exact repetition of the events up until that point, it is significant that Neo does not react: it means that this iteration of the Matrix is fundamentally different from the others.
When Morpheus tells Neo that he is not the first but a sort of reincarnation of the One in the first movie, the pattern is different from all other iterations where Neo only became aware of his predecessors when he met the architect.