From sequels to reboots or, well, just making anything successful in video game form whatsoever, nailing a creative vision goes through any number of sizeable changes.
Maybe you're a Hideo Kojima, a Corey Barlog or a Ken Levine and maybe there's a design doc full of reference points you can't stray TOO far away, but even then, chances are some unforeseen element is going to rear its head and upend everything.
Planned set-pieces get canned because deadlines come around too soon, maybe a physics model wasn't perfected so now an entire mechanic can't be leaned on anywhere near as much.
In the end, fans and critics alike can only analyse the product they've been given - that is, until word comes out of various forks in the road that could've gone a different way entirely.
Looking back you can often side with the creator when viewing a deleted scene or element; appreciating the larger whole they were striving for, but there are some ideas we're just glad didn't make it through.