Despite the quote from Gilligan, the flashback to Jesse lovingly crafting a box that he gives away for dope suggests that Jesse is doomed.
The episode makes the most sense as a dying delirium, instead of a series of real events. Briefly, too much of the episode was impossible. In its own terms, the plot requires that Walt dies of cancer in the cabin, and Robert Forster gets the money, and Jesse is a slave until he's killed, by his own hand or someone else's, Skylar's in jail and Marie is all alone. And, Todd, Deus Ex Machina made flesh, shacks up with Lydia.
In the end, the episode is jury-rigged so that Walt wins most of the control he sought so desperately rather than face his mortality and achieves courage and serenity in the face of death. For me, the finest expression of what Walt has really been about was his hysteria in the crawlspace. Undoing that, turning Walt into a brave man, is obviously a very popular dramatic choice. Obviously in that sense Gilligan has succeeded triumphantly.
Personally I can't help but feel that Walt's impotence when trying to tyrannize Saul, or manipulate Forster's character, should have been finished with his impotence in mastering his fear. Walt broke when he was diagnosed with cancer. I can't really believe that success in the empire business would regenerate his moral integrity.
I admit the pressures to glorify Walt must have been enormous. (And, I think that even if you were going to go that direction that the contrast between Walt's antihero and Jesse's antivillian really should have been key to the resolution.) Nonetheless, I don't think you can say the series ended well.