Dan Didio's been saying that the whole Captain Atom thing is somehow going to tie into Infinite Crisis, but in what context, nobody knows.

Bucky's death... was death, I still hold out on the "cosmic cube theory" that he was displaced from an alternate universe. I know, it's insane.
The bit you mentioned about Hawkeye, dead on (pardon the pun) about which camp to be in.

Jason not being dead takes away from Bat's. They say it won't, but it does. That's just my opinion.

I thought he already came back in the Supes/Bats series?

I agree.

Actually he was literally blown out of the DCU and ended up in the Wildstorm Universe.

According to the final solicits, a dormant Captain Atom is a big part of the Battle for Bludhaven. I'm going to assume this is after he gets done giving a much needed schooling to the Authority and returns from Wildstorm.