I've been watching the original cut of TMP recently and I've come to appreciate it more than I did when I was younger. That said, there are some oddities that I do have questions about...
1) Is there dialogue missing that explains the weirdness regarding Lt. Ilia? The crew get all weird when it is announced that she is Deltan and then we get that "oath of celibacy" statement...yet it has no context. Even in expanded versions of the film where she talks about "sexually immature species" its not really explained what she means. Is this a hold over from the Phase II pilot that would have been expanded more in the series?
2) Why is Decker (and Kirk for that matter) demoted for this mission? There is no reason why anyone needed to be demoted for this event. Indeed, its not totally out of the question for an admiral to take command in such a critical situation. In most instances the admiral would command the mission while the Captain would command the ship. We see this quite regualrly in other Treks and indeed this is exactly what happens in The Wrath of Kahn. No wonder Decker comes across as pissy for most of the film...there was no reason for Kirk to do what he did.
3) Where was Starfleet in this movie? The "only starship in range" is an old trope, but it seems problematic in the context of this film. Lets remember that Starfleet first becomes aware of V'Ger after monitoring the incident in Klingon space. That means that V'ger traveled between the Klingon Empire and Federation. Yet it never seems to encounter any Federation ships. Are we to assume that there are NO Starfleet vessels ANYWHERE between Klingon space and Earth? Indeed one wonders why the Klingons didn't try to follow and attack.
4) Why does V'ger fire torpodes on both the Klingons and the Enterprise, but seems to simply "eat" or disolve Epsilon IX?
5) Given all of the rereleases of older material with new edits, do we know what is considered "canon" about these movies? For instance...was V'ger's cloud REALLY 82 AUs or was it a mere 3 (which is still enormous...Earth should have been engulfed in the cloud long before V'ger arrived in orbit).
6) This is more of a trektech nitpick but it seems reasonable to point out....V'ger obviously has some form of FTL propulsion in order for it to cross the vastness of space. Indeed it arrives in Earth orbit from Klingon space in mere days. Yet oddly enough, both the Klingons and the Enterprise approach V'ger at impulse. How are they not getting "run over."