This is my understanding of the last scene. Decker says to Kirk I believe something to the effect, "as much as you want the Enterprise I want this." We are told in the motion picture why Kirk gets command of the ship, because of his experience, indicating that Decker is a less experieneced commander. We also see Decker as part of the central love story in the film and as a somewhat broken hearted individual. Perhaps losing the real Ilia, losing command of the Enterprise, and his family background, (his father sacrificing his life flying the shuttle into the doomsday machine) all lead to him accepting to merge with Ilia/V'Ger by physically entering the transmited signal and allowing the probe to 'touch' its creator. In this way Decker becomes the hero, getting the girl, saving the ship, saving the earth, by making this sacrifice in return he is rewarded by morphing into a higher human evolutionary life form and reuniting with Ilia.
