You're more forgiving than me. Probably mostly fans bought the novels even back then and fans I think always considered Where No Man Has Gone Before to be the first on screen appearance of the original series crew in the timeline (even if it was the 3rd episode aired). IMHO I think it was a mistake to seemingly ignore most of that episode. And she didn't totally ignore that episode because Gary Mitchell was mentioned prominently. So it made it very confusing. I'm sure many fans while reading it were thinking, Sulu was a physicist at the time, why is Dr McCoy there, Janice Rand?? and so forth.
Never assume all fans have the exact same experience of Trek. The whole reason that franchises branch out into different media is because the audiences for different media don't overlap 100%. There will always be people who are more into the movies than the shows, or more into the comics than the novels, or whatever. And the TOS movies had a major impact on the popularity and public perception of Trek. There were lots of people who knew Trek mainly from the movies and weren't that familiar with, or that interested in, the one-shot characters from the second pilot.
Besides,
Enterprise: The First Adventure was a big event. It was the 20th-anniversary novel. It was the first "giant" novel. It was promoted more heavily than an ordinary novel. So it stood to reason that it would attract a wider audience than a typical novel, and thus it was logical to make it more accessible to casual fans. Not to mention that a book that was meant to be a celebration of 20 years of
Star Trek should logically focus on the characters we care about most.
I was looking forward to a bridge between the characters seen in The Cage and Where No Man Has Gone Before.
That seems a bit odd to me, considering that there are something like 11 years between those two. Despite the conceit of the movies, it's unrealistic to expect that Pike would've held onto the exact same command crew for that long.
Unfortunately it's made it hard for me to look at that book as a true first adventure, and was a disappointment as a result. I know you mention the 2009 crew, and I know there's been debate about a basically green crew taking charge of Starfleet's flagship. But in that case you can argue that's a parallel timeline.
Isn't that beside the point? You raised the question of why McIntyre chose to focus on the TOS cast instead of the pilot cast -- the real-world reason for the writer's choices, not their in-universe justification. I'm saying that the real-world factors that shaped McIntyre's choice to focus anachronistically on the familiar seven main characters are probably the same ones that shaped Abrams's choice to do the same, and thus were not the result of ignorance of the second pilot. There was a logical reason to make that choice.
I remember Strangers from the Sky coming out not long after Enterprise: The First Adventure, and it always seemed that Margaret Bonanno Wander tried to fix some of the character issues--I remember specifically her explaining something about Dr. McCoy having to take leave and Dr. Piper temporarily relieved him.
"Fix" is a strong word. To be fair, there's nothing in "Where No Man" that
excludes the possibility that McCoy was there before Piper. Piper was virtually a non-entity in WNM. He just had a handful of expository lines and we learned nothing about him. Whereas when we first met McCoy, it was clear he and Kirk already had a well-established friendship and history. So it actually kinda makes sense to have McCoy there first and treat Piper as just a temporary fill-in for one episode. There's nothing there that needs to be fixed. Indeed, since McCoy is about a million times more interesting than Piper, I'd say that putting him there in Piper's place
is the fix.
Mike Barr did the same thing in DC's earlier (and much better) version of "The First Mission," having Kirk recruit Bones to the crew when he first took command -- although he threw in a line establishing that McCoy would soon need to take leave and let Piper fill in for him. He also included Uhura in the story instead of Alden -- though he made Sulu the astrophysicist, left out Chekov, and included Mitchell and Kelso. Mike recognized the same thing that Vonda McIntyre and J.J. Abrams subsequently recognized: That audiences would be more interested in McCoy and Uhura than they'd be in spear-carriers like Piper and Alden. Though he struck more of a balance between the pilot and series casts than the others did.
). They sort of fall into the camp you described, as a different interpretations viewpoint. The original series novels seem to fall into that category a lot of times, even still today. 
