The biggest weakness I saw, was that they didn't deal with Dr. Mahattan's ability to appear at multiple places at one time. He has the foresight to leave his powers in an egg (which seems like altering the timeline beyond destiny anyways). Why wouldn't he just make a copy of himself that doesn't rush into the battle with the fancy ray gun.
Pretty great finale, as it did an excellent job of wrapping everything up, which was actually a pretty big feat considering how random it all was. Maybe it's just best not to overthink the Manhattan stuff.
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