But this gets back to the central problem with the film — I believe articulated by Harold Livingston —that was that they set up this godlike being of effectively infinite capability and for our heroes to have any sort of relationship to it undermines the premise and makes the premise inherently false.
It would be interesting to see what Livingston said.
But, yes, I agree this is a problem. It's a problem because the writers seemed to take seriously the idea that V'ger had reached the limits of knowledge in this universe. V'ger clearly lacks an understanding of what "carbon units" are, and what machines are, for that matter (at least in the case of machines from Earth), so its knowledge of what's going on in the universe is demonstrably incomplete. The premise is therefore absurd. The idea that higher dimensions are needed just for V'ger to be able to get to something new is equally so; V'ger was unfinished with these dimensions in the here and now.
But it could have been the start of a position regarding hubris: V'ger thinks it knows it all, but it doesn't. It's a shame that wasn't an aspect of the conversations among the main cast. Naïveté wasn't V'ger's only flaw. There was ignorance, of course, but also arrogance. An ability to leap beyond logic wasn't the only human trait that V'ger needed (in order not to be a danger to everyone). The premise that V'ger acted like a child implies that it also needed plain old emotional maturity.
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Getting back to the list in the OP (it's a good list,** by the way), one thing that's always bothered me in the film is how the
Enterprise survives a hit from the plasma weapon when everything we've seen so far hasn't. I get it: the ship is still in peril because we are told that it can't handle another attack, and this is showing us that the ship has been upgraded. Plus, it's not unreasonable that even V'ger's technology has limits. But V'ger has scanned the ship, it's super-advanced, so the idea that it wouldn't send something capable of penetrating the shields is hard to believe. We are told later that (at least in Spock's opinion) V'ger seems to have scanned whole galaxies, and since there's only one way we've been shown that it scans things, presumably those galaxies were absorbed the same way that the Klingon ships,
Epsilon IX, and Ilia were, but by an even larger-scale version of the process.* So, if V'ger can eat that much, it just doesn't make sense, especially this late in its journey after it's become extremely experienced, that it would miss on its first try at the
Enterprise.
How to fix that? We already know getting hit by the weapons is bad news. Just have Spock realize that V'ger has been trying to communicate*** and send the reply before the first missile hits. V'ger shuts it down, and Spock has saved the ship. Oh, and Uhura should have at least helped to have figured some of that out.
* - Arguably that's also dumb, but I don't really have a problem with it. It strongly necessitates that the black hole threw V'ger back in time as well as to the other side of the universe, though. That way, V'ger has time to wander the universe and eat whole galaxies before returning back to the Milky Way.
** - Regarding some of the things on the OP list, I never had a problem with the Klingons attacking the cloud. By their broadcast, they have identified a vessel inside the cloud, and they are trying to repel an invader in their territory. No doubt by Klingon logic (and some human logic IRL), V'ger's destruction of the attacking ships is evidence of it being a threat.
Also, the black hole that V'ger fell into could have been one of extragalactic origin, just passing through the solar system or near interstellar space with high proper motion (improbable, but not impossible). Sure, it would have been better to have said that, but it's not really "dumb" in the same way that most other things on the list are.
As for the only starship in interception range thing, this can be mitigated by having V'ger approaching Earth at high speed.
Enterprise is "in range" because it's approaching V'ger from the direction V'ger's headed in. The central problem here (not mentioned in the OP article AFAIK; oh, and, ha ha), is that if
Enterprise is the only ship in range, then there isn't any other ready starship in Earth orbit at all! WTF?!? I agree that it would have been an improvement to have sent another (Federation) ship in ahead. Spock can even have received scans to analyze and discover V'ger's attempts at communication from long range as the other ship goes in. So, the two attacks are split between two ships. Spock doesn't discover the high frequency transmission in time to have saved the first ship, but forewarned the
Enterprise is ready when they arrive at the cloud.
And:
*** - As to what V'ger's communication was that Spock replied to to save the ship, it could have just been V'ger's version of linguacode. But yes, that absolutely should have been followed up on.