Here is my standpoint on how the Second Shivan Incursion would have went if the NTF had not existed (disregarding, of course, that the NTF started it in the first place):
Facts:
1. The GTVA would not be fighting two wars at the same time.
2. Terran-Vasudan Relations would be improved (destroyed by NTF).
3. The Colossus and many other destroyers, cruisers, and corvettes would have been able to focus their firepower on the Shivans.
4. There would not have been large losses of people and ships, both due to NTF defection and GTVA death toll (and, of course, NTF defection combined with death).
5. The GTVA would have been in a slightly less mobilized situation.
6. SOC would not have been focusing missions on NTF infultration and therefore would have been able to focus more on Shivan infaltration.
Opinion:
Although it is true that the NTF put the GTVA in a war mobility state, they also caused severe damage to the GTVA which made the war worse.
However, thanks to the NTF, the GTVA now has the Knossos device blueprints. In addition, nothing is known about whether or not Bosch succeded in communitacting with Shivans and what happened through that.
Final Conclusion:
FS2 happened the way it did. Shivan return was obvious, but not at the start. In fact, it was pretty much a FS theme: start the game with an ongoing war, then throw the Shivans at us. In FS1 it was the Terran-Vasudan war, in FS2 its the NTF. (Of course, in FS1, the Terran Vasudan War ended, but was replaced with the HOL).
Since we will never really know what [V] planned to do with the storyline, its best to disregard it.