I think the only really big reveal was the whole Walternate angle. I mean, you had to be very dense to miss Peter being from the alternate dimension. Hell, that was explicitely revealed halfway into season two for the slower members of the audience.
They can easily get a third season out of the existance of the duplicates of everyone, and if they really want to drag it out, a fourth out of taking the fringe war to the other side.
Of course it does put a crimp on the 'random but fringe' stuff they do to fill out the seasons, things unconnected to the other side. I'm not sure the alternate universe really explains the 'pattern' either, but that's been an 'also ran' sub plot for a while now.
Lastly are the observers, who are NOT connected to Walternate, and whom the fringe team has not managed to learn anything about.
Yes. I have hope. But my faith in hollywood to fuck it all up in a single night of rage, er... bad episode... is strong as well...