Yeah, I wouldn't call those plot holes. Fury's eye story was meant to be an embarrassing thing played for laughs which he simply builds up as something more than it really was. As for the Skrulls being good, we are simply introduced to them now and frankly they are generally nicer than the Kree are in the comics. There is still time to give them a villainous bent, but even it they don't, it wouldn't be the first major change between the comics and MCU. I mean MCU Mantis is practically an original character compared to her comic version and Star Lord's dad is not Ego in the books, so there is no real issue here. If you want an actual plot hole it would probably be the retcon to the Tessaracts history within the MCU because the first Avengers movie gives the impression that it was discovered along with Captain America, but Captain Marvel now reveals SHIELD has had it for decades.

As for unreliable narrator, I feel you're off on what the term means narratively speaking because it only works when a story has an actual narrator or point of view character. In the case of Star Wars, Obi-Wan lying to Luke about his dad is explained in the film as him trying to protect him as well as hide his own shame. While the whole reason to add all of that in was simply because Lucas hadn't quite decided to that twist until then and needed to cover for what was stated in the earlier film because he was kind of writing the plot as he went and trying to avoid plot holes. So there is no actual unreliable narrator here especially since the Star Wars films don't really have a narrator like say... Big Trouble in Little China or Rear Window. The latter being a more pure example of what an unreliable narrator type story really is.

The issue with the prequel films... well that's a huge can of worms to really try to unravel in one post, but it's basically a combination of Lucas making some questionable retcons to the series and mostly the fact that he can't really write as well as he thinks he can, and the films needed some trained script writers to punch them up like what happened for Empire and Jedi. That love story is just a mess...