I've always thought so, too. It seems like all of these events didn't start until after Walter brought Peter here. And if I were alter-Walter, I would've been furious that my kid was taken to another world.
Just a hunch, but I think that Peter might be a big part of the reason for the war. Many have theorized that Walter is crucial here, but I think Peter might be even more so, after all he is the only one we know who is actually from the other universe. My very early theory is that part of the reason for the conflict is the imbalance created by other Peter being brought to our universe. Maybe other Walter is mad? I still want to know how all the experiments Walter was doing tie into this, such as the ones with Olivia..other than the obvious that they were trying to create soldiers. Just an idea, tell me what you think.
I totally agree with you, BW and K. I think Peter's real skills, little by little, have been brought to the storyline. Surely, he has a huge part on the whole "mess".
"There's something important. Oh! I've decided on the pancakes...blueberry." Walter Bishop