1. I assumed the Borg's memories of their own origins were damaged. In any event, this might be an "inconsistency" but is hardly a "plot hole", and if that's enough to damage your opinion of the trilogy then I don't think the problem lies with the books.
2. As the Caeliar never ultimately define what they consider more advanced than themselves, it's possible those species wouldn't qualify. Alternately it's possible they had no interaction with those species. Heck, it's possible those species deliberately took steps to evade detection by the Caeliar.
3. It's possible the natives of Kintana found ways to expedite the process, is it not?
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.