So we have two options:
1) Show that is different from original conceptualizations and may not have perfect flow in a couple places but overall is better.
2) Show that is identical to conceptualizations and has good flow, but suffers from distinct lack of quality of show.
It is a lose/lose situation and so they pick the one that satisfies the largest number of people and keeps the overall quality of the show pieces maximized.
Films do this too. But since you have never seen the film in it's first cut, you have no way of knowing what could have been and therefore can't compare and complain about this or that cut. Then the DVD comes out and the "deleted scenes" are shown and suddenly you wonder why this or that scene was cut. And seeing those you can go back and watch the film and see where cuts and edits happened and how sometimes those don't flow as well knowing what could have been.
Knowledge is a dangerous thing.