Wasn't it mostly the outer rim of the island? I mean we only know from what we saw from the Boat, but I would have liked a better explanation for why there didn't seem to be any evidence of a bomb rather than what we got. Also, it's been 2 years, which seems too short a time to grow any kind of vegetation.
They seemed to be saying that the "energy spike" Novu's device tapped into was responsible for resurrecting the ghosts and restoring the island along with them. I guess it's some kind of phenomenon distorting time and/or reality, which is why it's useful to the Monitor, but they could've explained that better. They seemed to be just going through the motions with a lot of this, like they're just marking time before finally getting on with the Crisis.