Had some time to think about my first playthrough. Will just list off a few things.
I think the way the game tried to move the party from point to point felt really awkward throughout. Using robed individuals didn't work too well for me and I constantly had to tell myself to not think too much about each instance which is not a big deal in isolated instances but when it's constant it's more problematic. When they were left behind between ch.9-10 I thought things worked notably better even if the party was just tackling things as they came along. I think this had a pretty notable impact on my investment in the plot.
I think the game is consistently excessive with its story beats. I think it worked really well for parts of the game that's just having fun. Upper Junon, Shinra 8, Costa Del Sol, Gold Saucer, side quests, etc all were great and benefited from all the extra flair. I think it was a lot more mixed when that same excess was extended to the more serious story beats. The first instance where it felt like it was a net negative for me was Dyne (I think Dyne/Barret stuff was mostly fine, but presence of Shinra in its entirity was a clear negative for me), and it was very hit and miss for me from that point on all the way to the end.
On the other hand, I think they did an amazing job with the characters again. While I thought the plot was not on point at times, I think the interactions between the characters of the main party were consistently great. While I thought they fumbled a lot of the little details with scenes driving the plot, I thought they nailed vast majority of the details in regards to character interactions and continue to add great depth to them. I mostly wasn't invested in the plot by the end, but I was still very much invested in the characters, and that's probably enough that the game nails just one of either the plot or the characters for the story to have enough pull.
I felt that the Zach parts of the story was ultimately irrelevant due to how it was used in the end. During the game I thought where Zach's segments happened was pretty well placed and while it moved fairly slowly I thought it worked well in contrast to what the main party is doing at the time. After reaching the end I feel like if Zach's segments were removed entirely I don't think it would impact the plot or the characters in the main party much, if at all. If they have plans for him for part 3 then that's fine but I think he didn't need to be in part 2 in hindsight. Similarly, I thought all the different timeline or multiverse stuff were largely not meaningful. I think the same story beats could have been accomplished even if that stuff was absent.
I am fairly content with how the game ended, but I am quite a bit more negative with how the final part of the game played out. It's again an issue of excess that made the story beats at the moment lack the focus that helps reinforce an emotional attachment for me. I think they tried to do too much for the final battle and couldn't focus on an emotion that they want to convey for any single moment, and that moment was changing extremely rapidly due to how much back and forth was happening. After the dust settles and all the fights were over I think the last couple of scene to the credits handled things a lot better. I think they did a great job with conveying the situation with Cloud at the end and gave the scenes proper amount of room to breath so the emotional impact can come through. I also think they did a good job with what scenes to include and what to omit to drive some degree of suspense. I think it would be beneficial if the more serious plot points have a moment to reflect on itself, and that's all I think I need which can easily be accomplished if the bombast is dialed back a bit.
Overall I enjoyed the story dispite a notable number of issues that I have with the plot. I'm very much still attached to the characters and want to see things to the end with them. Also, I very much enjoyed reading/scanning (most of) this thread from beginning to end. A lot of little deatils I missed or weren't aware of were filled in which helped a lot in processing my own experience.