Well there is some precedent, since Bryce gave Chuck a pair of intersect update glasses at the end of S1 (or sometime in S2?), but yeah - the show plays it fast and loose with most of the mythology and serious stuff. As the writers have tried to one-up the previous season's threat at the finales, the whole thing has sagged under the weight it can't support. Its actually kind of jarring rewatching the pilot now, so I can imagine going through the entire series in a short span highlighted the shift.
But its tradition now for Chuck to throw a big twist at the finale, so might as well get to the conjecturing. I wouldn't be surprised if the Morgintersect wasn't a complete version; either just the information (like the original) or just the physical stuff. And I also wouldn't be surprised if Chuck gets all or part of his back, either. I remember the new antagonist agent - lets just call him Dick - specifically referred to his glasses as a supression device. So maybe between the 2 of them they'll have both pieces of the 2.0 intersect.
Its probably for the best that this will be the final season, and that the writers know it from the get-go. Having to plan the last 2 seasons without knowing if the back half would be picked up compromised the story arcs I think, but either way the end of season 2 was definitely the high point in my mind. Hopefully they get back to what made the show good and end strong.