I think it's possible to see flaws and yet enjoy the ride, especially due to the views. I also think that the ride promises Yoshi's Island due to the fact your ride vehicle is a Yoshi, it plays Yoshi's Island music, and the typography, queue, and a very short scene in the attraction are Yoshi's Island themed. I just think that the buildup to seeing the Yoshi's Island scene does not match with what the interior scene delivers, not even that it is stylistically different.
Look, if I were designer, and if the conceit is that each time we go through a warp pipe we were jumping back and forth between Yoshi's Island and the Mushroom Kingdom, then as we re-enter the loading dock, after Captain Toad congratulates us, I'd add a simple scene of Yoshi looking on towards the sky and seeing the Stork fly away with the two brothers, or else something to show that Yoshi had a Successful Journey. Normies would be like AWW look at the babies! Fans would get the reference. Look, as much as I'd hate it, paint it on a wall like Snow White. It'd be the payoff to the bizarre mid-ride interior scene, and a payoff to the name "Yoshi's Journey". I just think this is the ending the ride deserves. It's like the hot dog scene with the sneeches. Not mind-blowing, but it's good storytelling and leaves you with an "aww".
EDIT: I agree with the above, the MK queue is insane and gorgeous. Just from the POV, and obviously never having ridden it, I think it's buildup and pacing is wildly perfect, feels like stepping into a real game. Will probably top the charts for favorite queue ever, or at least top five-ish.