At the end of Fringe's third season, there was a significant change that you might not want to know about if you haven't viewed that far, so this is some introductory text to give you a chance to avoid reading any further. This question is composed of spoilers (for season 3 and earlier), so stop now if you wish.
In the original timeline,
William Bell altered Walter's brain to remove knowledge of how he'd created the dimensional bridge, resulting in Walter's mental illness.
Is this the case in rebooted timeline? With
Peter having died in the pond rather than having been saved by the Observer,
it's not entirely clear whether this will still have been the case. Walter seems as odd as ever - though this may be the message the writers are trying to convey, that it was Walter's destiny to end up dysfunctional, one way or another.