In any event, none of these strike me as things that should ruin one's opinions of the books...at worst I'd call them head-scratchers and, shockingly, questions to ask the author before judging his work. They certainly don't constitute "plot holes", as points 1 and 3 have no bearing on the plot, and point 2 could easily be addressed without altering the plot.
And I agree they do not necessarily "ruin" a book just as they do not necessarily "ruin" and episodic television show such as "Voyager". It's the math one that pulls me out of the story. We are told that the Caelier are xenophobic, that they do not associate with species they believe less than themselves as those species would "expect" help. The same help that the Caelier expected to get for themselves from a superior species.
I have already given the Caelier the benefit of the doubt by allowing them 15 years to shroud a sun. But math says that the Caelier would have to shroud a sun in less than Seven years and all this from a species that refused to travel faster than the speed of light, and refused contact with species deemed lesser than themselves, and at the point of time that Kintana exited their subspace tunnel there was very little chance that any species was more advanced than themselves (unless those species like the Q had lived through the cycles of the Universe). Just the fact that they wouldn't travel faster than light alone makes even the 15 year estimate impossible too.
The fact that you have come up with a plausible assumption doesn't mean that these are not plot holes, your act actually proves my point that they are.
Plot holes are not in and of themselves a mistake, but are a loose end, and I am always glad to find them because plot holes can be used to a great advantage by other writers. The problem with plot holes from the authors standpoint is that it leaves something open that other authors can take advantage of.
My favorite "Voyager" plot hole appeared in "Unforgettable."
CHAKOTAY: But you say we've met before.
KELLIN: About a month ago. I spent several weeks here.
If you check the star dates, "about a month ago" would have landed Kellin on Voyager right in the middle of "Killing Game." Fic writers love plot holes, they can be exploited to great advantage. Plot holes leave openings for other interpretations.
King Daniel wrote:
The Caeliar probably learned time travel after being hurled back through time. Harnessed, this ability allowed them to build their spheres in no time at all.
Except in the Books we are told that the Caeliar already have time travel and that ability was what the Columbia MACOs were trying to use to send Columbia back to human territory and in the "proper" time. The Kintana Caeliar even went so far as to make sure that their planet and sun were destroyed to keep from changing time.
For the Kintana Caeliar to use time travel would involve a complete turn around for their group, and that idea would be another exploitation of the plot hole.
My biggest problems with Destiny is the math problem and the way Deanna's pregnancy was used to build tension. It was soap opera at it's worse, and completely unbelievable for me. In discussions with other females in my circle, it is a problem with some of them too. I could not suspend my disbelief, that she would be allowed to go anywhere except home, and never on an away mission to an unknown and shrouded planet.
I had one other big problem (yep I had a lot of little problems), and that is at the scene of Picard lying on the Enterprise's bridge floor sobbing. I cannot even imagine that happening ever.