I'm waiting for the inevitable turn of events where Walternate shows up in our timeline, and has to pretend to be Walter to avoid detection. It will be fun to watch someone accustomed to being treated with utter respect and no small amount of privilege trying to fit in Walter's shoes. I'm curious to see where he would finally be found out as a different person.
As for Olivia on World B, I'm hoping it will still be quite some time before she's brought back. The suspense of her trying to avoid detection by her mother and colleagues will make for some good episodes, though maybe they'll try and avoid what they're already doing with Olivia-B, whose agenda is more sinister than simply trying to get home. Then again, it would be an interesting parallel to have us rooting for her to be discovered in our timeline, and hoping for the opposite on World B.
As for the overall "We're at war" excuse Walternate gives for his actions, I've been at a loss for how he can rationalize it. He's devoted a huge portion of government resources to publicly battling the rifts and secretly toward waging war on another reality. The rifts are likely the aftershocks of Walter's initial tearing of the veil between realities, and any other tearing that occurred after, such as the German from "In Which We Meet Mr. Jones" and likely Walter's own rifts caused by sending the shapeshifter/android troops over. How can he rationalize continuing to invade and covertly kill World A people when he knows everyone in World A is ignorant of the rifts. Or does he?