I think paraphrasing Yoshida sums it up best, the writing team doesn't have a plan, they are allowed to do basically whatever they feel like. When you have a persistent writing team that's fine, but when the pen starts changing hands things tend to go awry. Like going on an expansion long side quest and coming back to the war you were in the middle of being finished unceremoniously off screen or having ten years worth of story wrapped up by a Woobie destroyer of worlds whose specialty is previously unheard of space/emotion magic who pops up in the last third of the expansion.