I think open war would have been much less likely if V1 was in charge, but that the Anis would have been more likely to die. So would that have been better or worse? Certainly the Anis couldn't handle open war for very long, and a quiet invasion would make it easier for them, but V1 is more competent and wouldn't underestimate Humans nearly as much. They definitely would have had to go into hiding much sooner.
If Rachel went out with Marco, there would likely be less drama in her life. Less stress. However Marco is less moral than Tobias, which could cause more damage to her psyche. Unless his jokes carried her through. After all, he did go through the least amount of change in the war, I believe. That could have helped rachel.
Tobias and Cassie? Well I believe they are the two most moral members. Seeing how Cassie survived the war, Tobais would have been better after the war was over.
I don't know how Jake and Tobias would have been different if they were raised by each other's families.