The fly-over of the refit Enterprise not only establishes the new design and serves as a "thank you" to fans who helped to bring back the franchise, but it serves to establish a sense of scale of how big the ship really is. First, you have Kirk and Scotty; knowing how tall they are, you can extrapolate the size of their travel pod. Knowing the size of the travel pod, you can see how big the Enterprise is during the fly-by and the docking sequence. Finally, knowing the approximate size of the Enterprise, you get a sense of just how huge V'Ger really is. In the novelization, it's stated that the Enterprise approaching V'Ger was analogous to a mosquito approaching the Enterprise.
What exactly was going on in The Meld at the climax is puzzling until you realize that the light surrounding Deckard and Ilia was the light probe V'ger used to "collect data". However, unlike the previous probes, this one is slower and gentler, because V'ger doesn't want to "collect data". It's using the probe as a transporter beam to merge him and Ilia AND ITSELF.
Kirk's efforts to mend bridges with Decker after bumping him down from Captain to Executive Officer are helped somewhat by the fact that his relationship with Spock seems to have ended between the Five Year Mission and Spock's return to the Enterprise. If Spock and Kirk got on from the start as well as they did during the original mission, he would have likely pushed Decker further away, but instead Spock's behavior leads Kirk to be unsure of his reliability, and he thus has no option but to continue relying on Decker who, by Kirk's own admission, has been proven correct on several of their disagreements.
It's an old bit of fan wisdom that Spock and Bones represent the two sides of Kirk's personality. Doctor McCoy is his emotional intelligence, and Spock is his intellectual curiosity. At the start of the adventure, Kirk is charging blind and causing chaos with his crew, too blinded by the urgency of the situation to see potential problems coming. Doctor McCoy beams up and begins calling Kirk out for his hubris and pointing out the damage he's causing to his relationship with Decker. Then Spock arrives and begins methodically approaching their problems as questions to be solved. With the old Power Trio back together and getting back into sync, Kirk finally has his wits about him again and is able to captain the ship properly.
Throughout the film, the Deflector Dish of the Enterprise glows both amber and blue at different points. However, if you watch carefully, the dish glows amber when only thrusters or a tractor-beam is moving the ship, and blue when it's under either impulse or warp power.
V'Ger's "entire journey" becomes a lot scarier when one takes into consideration that V'Ger basically murdered countless innocent races as it absorbed them in its quest for knowledge.
On a more meta level, Kirk pushing Rand out of the way during the transporter malfunction was a serious error in judgement (that was most likely dictated by the writers working around Shatner's ego). At that point, Rand had likely been a transporter engineer longer than she'd ever been a yeoman, and although Kirk probably understood the basics of how to operate a transporter system, it's highly unlikely he would have had the specialized systems knowledge that she'd have acquired in the five or so years she'd been doing it. If there was still a chance of saving Sonak and Ciana, Kirk taking over the console probably doomed it. (As it was, subsequent appearances of Rand in different departments, and eventually as Sulu's first officer aboard the Excelsior, make it likely that the trauma of the incident ended her career as a transporter chief on the spot. Kirk's actions would not have helped.) Likely the only thing that saved Kirk's career was that in the rush of dealing with the V'Ger crisis, no one bothered to check the event logs from the incident.
In the novel, Kirk actually dwells on whether he should have done that, and that he was not proficient at operating the console. It's a bit strange that the movie doesn't highlight this at all, considering it's the exact same theme of Kirk swooping in to take command of the Enterprise that he's just not qualified for. Certainly it seems Bones should have brought it up when he was questioning Kirk's motivations and behavior. Two people died because Kirk was demanding engineering go faster, and then he butted in during the accident and took the controls from the certified operator.
