Shit, it's late and I can't read.
But again, I still don't see how that makes sense since Brotherhood (at least so far) takes place during the game, and Kingsglaive as well. Unless the Insomnia invasion was somehow worth a sequel, which seems unlikely.
I imagine Brotherhood being mini-stories that would've been "major character sidequest" in the game itself that got cut and turned into anime series. That probably isn't a huge detriment and it's simply a conscious decision to adapt stuff that didn't fit in the story flow very smoothly into a multimedia anime.
As for Kingsglaive, I think this is where the expectation of the original VsXIII concept was probably too much for the team to chew.
Put it this way.
The "Insomnia Invasion", as we knew it from VsXIII, was very likely the prologue of the game where Noctis was there, was part of the invasion storyline, but was defeated and forced into running, leading to the roadtrip section.
In Kingsglaive, just the "King Regis" part of the story itself was long enough to merit a 2-hour movie. I imagine that that if there was a storyline involving Noctis in the original script, that would've extended the original Imsonia Invasion concept to a 6-10 hour long prologue that ends with Noctis escaping the capital city, ala FFVII Cloud and co escape from Midgar.
I also imagine that the "end game" of FFXV would be Noctis returning to an occupied and heavily damaged Imsonia, caused from the fallout of the invasion to... "reclaim the throne."
I can imagine the team debating this and thinking "wait, we have to create TWO SEPARATE game assets for Imsonia, one for prologue invasion and one for end-game?" As well as craft an Uncharted-tier set-piece bombastic prologue arc that is effectively used up for that 6-10 hours, and then loop back into the final part of the game again from scratch.
And then making the decision to say "let's just make one of those, aka the end-game part, and take that original prologue, scrap Noctis out of it, and give what remains to another team to make a movie out of it."