While I don't mind the greatest hits compilation of the Yoshi ride, I don't think it would be unfair to say that a ride like Seuss Trolley (the good vehicles), Storm Force, Kang and Kodos, or even One Fish Two Fish have a more cohesive story. While I really love the outdoor scenes of the tiny Yoshi(s?) screwing around, I tend to agree that one more interior scene (as in Seuss) would serve the attraction well.
I'm never gonna find an excuse for that queue, space limitations aside. I despise being so close able to touch the wall that is supposed to be "sky". Breaks the careful immersion that is done literally everywhere else in the land. Reminds me of the awful Buzz Lightyear queue where everything is a printed graphic, with shades of Maelstrom's old queue.
As for timelines, I appreciate the way they are throwing everything into the pot. I even think that the "warp pipe" you go into could signify going back in time to see the Baby characters. I just feel like the animated figures, ESPECIALLY Yoshi depicted mid-run, are a big sore point for me. I think the main reason for this, though, is that you have some really well-done characters just outside (The Piranha Plants are SO real, the walking characters outdoors ACTUALLY walk, everything is so full of life) and inside for some reason there is a real disconnect. I think this would have really worked if they did a hopping animatronic like the Brers - it just really feels plastic-y in that scene. However. I think the story other than that is just fine. You need to get three eggs, they lead to the Golden Egg, Captain Toad is counting on you! Here, ride a Yoshi. A small nitpick: I think by calling it Yoshi's Adventure they set up that this ride will be about the plot of Yoshi's Island. I know it's longer, but Yoshi's Golden Egg Adventure could be more accurate, at risk of being far more clunky.
EDIT: I think that it's just as important to state the praises of the attraction. The interactivity is STELLAR and PERFECT for this attraction. It reminds me of the inventiveness of One Fish Two Fish, which I think is a genius component. I also think that NOT having a sky tram ride in this location would be absolutely bonkers, considering how incredibly immersive it is. The more ways to get bang out of that incredibly realized world, the better. I think everyone has ALWAYS wanted to ride a Yoshi, and this is the best way to do it to include EVERYONE. Sure, accuracy would be better in a "steeplechase" attraction, but this allows grandparents to ride with their kids, something Universal as a whole NEEDS. I really love the Toadette queue scene, and I think the pecking scene is awfully cute. I've seen a photo series where a Yoshi tongue fully extends from his mouth to catch one of the fruits, and I can't see it in any POVs yet. I thought it looked wildly realistic, I can't wait to see it again. I love Captain Toad at the end, and the music is such a bob the entire way through.