I'm sure they are going for a way to merge the universes. After all, the "orange" one is how things were supposed to be, had Walter not stolen Peter.
I thought Walter still steals red universe Peter, but the Observer doesn't save Peter from drowning in the orange universe lake, which is why the older version of Peter supposedly reappears in the same lake.
...and yes, you've got to ignore the bad science - a given for nearly all TV and movie sci-fi in any case - but the clue is in the name Fringe
. I well remember all the nutty ideas that were floating around in the 70's.
Frankly, I'm surprised Fringe
has managed to last four seasons. I had put it down to Anna Torv being James Murdoch's cousin, but that's just me being very silly.