In Guild Wars we first learned that magic was a gift from the gods. We then learned that it was actually given to us by Abaddon, and that this was a sore spot among the god-race.
Then EOTN came along, and, as mentioned above, it was intended to introduce the lore of GW2 and kind of guide us into the mindset of understanding the broader world of Tyria, beyond the lands and cultures of the humans. We learned that Tyria existed before the god-race arrived from their extra-worldly planes in the Mists, and that magic existed at least in some form along with the dragons that fed on it. The data that was given to us at the time GW2 started indicated that the dragons are part of a sort of cycle of magical consumption and excretion, and that as they slept, the magic they had consumed was released back into the world for the races to use.
We have also been guided into understanding that magic is more complex than just the four schools that the humans believed the gods gave them. Asura make use of magic in several different forms. That being said, all the knowledge and research of the Asura never even hinted at the existence of ley lines. We are now being told to accept that, even though they realized that some waypoints worked better than others, they never bothered to figure out what was right beneath their little pink noses. This is the brainiac race that researches every little anomoly they encounter.
My guess is ley lines were not conceived of before launch, or even six months afterwards. It's not the only paradigm shift we've faced in understanding Tyria, but is a more abrupt shift with no transition into it. It also has a very different flavor from the prior understandings.
Getting back to the OP, the problem with the Sylvari is similar because it also represents a dramatic change of flavor. In EOTN, the advent of the Sylvari was totally incidental, with Ronan finding the seeds and bringing one to Arbor Bay. The Pale Tree was nothing but an oddly shaped sapling, so now making it the heart of the cosmos, when we know perfectly well that everything existed before the seed was even planted, makes utterly no sense whatsoever. This is an even bigger issue than the ley lines, because it is directly contradictory with the prior data that we had.
But whatever, I'm still enjoying the game, so let's see what they do with these new twists.