Yeah, the big weakness of W's ending is that it all seems to really come out of left field unless you've seen the movie. If you slot the move into its proper place in W's viewing order, I think after episode 44, then it's a bit clearer what the show is doing and how the tone is shifting gears.
(I also think the movie thing is probably why W's ratings slide after the defeat of Terror. People who didn't want to see the movie or who didn't know that it introduced the NEVER stuff probably found the last five or so episodes really confusing and frustrating.)