From what I can gather, the writers admit that by the end of Season 2, they felt like they had painted themselves into a corner with the Rambaldi storyline. It was a bold move for them to just skip ahead two years. Their hope was that in season 3, because there is a two year disconnect, all of the storylines could start afresh with only some reference to the past. This way, new viewers would find it easier to get into the program. Slowly, they would then fill in the gaps.