I'll start with saying I am relatively forgiving with the story being a bit (IMO) underbaked given the circumstances. I've mentioned a few times that I'd guess the reason the story turned out how it did is one part due to budget and another due to planning, but that's not the point of this thread and I'll leave it at that.
I actually don't mind if S3 was never intended to push the main story forward very much, but with the story we had, so many plot reveals between point A to point B were underdeveloped and odd. If everything that was in Shenmue 3 was properly fleshed out and well executed, I would be absolutely happy with the story overall. The first interactions with new characters were too brief, it feels like almost every cutscene was truncated in some way, and there was this really weird lack of urgency in a few moments ("gotta go stop the thugs that I know are up that path right now, but oh wait, I guess I'll play hide and seek!" and "The thugs took a hostage and are staying put in this house for some reason for days on end! I'll let them chill there for a few days and save the kid at my convenience since they'll just stay at that same location 24/7").
I would also agree with
@iknifaugood that there's a bit of a disconnect between how the idea of training is implemented in the story, especially compared to Shenmue 2. In Shenmue 2, you're being taught martial arts philosophy and ethics, discipline, and yes, some new moves like in Shenmue 3. But the difference in Shenmue 3 is the act of "learning" those moves is functionally there to just gate the story. There's not really the sense that Ryo is learning things like any martial artist of true virtue should know (like the wude).
I do think that everything that was there COULD have been interesting with better execution and a bit more development. Some of the ideas were there, like coming across the old training grounds of your father, learning more about the phoenix mirror from the local yokels, being trained in this ancient rural martial arts focused town, Li Feng actually being Niao Sun and then double crossing Lan Di and essentially causing a rift between the Chiyoumen. There's part of me that would have really enjoyed if Bailu village taught Ryo to relax and have patience, and have some more time to reflect on his life and choices up to this point.
While we didn't learn too much directly about Shenhua, I still would say that the chats with her contributed positively to the overall story. There are also a few small and easily missable lines of dialog she had, (which will be paraphrased and butchered going from here) like when she mentioned she feels like she has the memories of many different generations of people, and that the Shenmue Tree's flowers are in bloom but will die out soon. I think this supports some of the theories that Shenhua is reincarnated. I'm hoping that during another playthrough I can find a few more of these small moments.
Overall, it is a bit frustrating because there's not really a way you can have a do over of the story. I'm just hoping then can make some big improvements for Shenmue 4.