Well until the databook was released, we had no idea what Shinju was nor what happened to Hamura.
Then Orochimaru's motives were unclear.
The connection between Spiral Zetsu and Obito and why did Obito act like him even in front of Zetsu.
It was never explained what the new unique power that the EMS unlocks was (as stated by Itachi, no it was not eternal light).
The mystery behind Hashirama's death.
Mystery of Uzumaki's annihilation.
There were more that I can't recall.
There are only a few people that liked Kaguya and the ending for whatever reason. Not to be mean, but you have poor taste if you think that made the manga better or you thought her character was good. You can't have a good character that says nothing, has no real motive, or has little to no connection to the protagonists.
There were minor characters (like Ao) that had more development and dialogue than Kaguya (who was the final villain of the manga). That is the very indication of terrible writing.
Orochimaru is irrelavent and has nothing to do with the main event of this war.
Spiral Zetsu is Tobi, we already know the connection with Obito...
Every EMS users have different ocular power. Madara and Sasuke have different set of sharigan capabilities and their tomoes design are different , Madara explained about sasuke choku tomoe which he can only posses amatarsu. Simply put it gives you enhance power to evolve something even better like Perfect Susanoo. Sasuke with EMS has been show to easily manupilate his amatarsu into a sword, or Susanoo Kagutsuchi, etc.
Hashirama death was definately a mystery but it was never expected to be important
All these mysteries you listed are either non-factor to the main Plot or it's been answered which already fulfilled. The only mystery that I agree which should've been explain is the Uzumaki annihilation.
Of course you would say I have bad taste because I'm one of the "minority" to like Kaguya and of course she has no development when Kaguya was revived at the end of this series but Kishi was forced by Shonen Jump to end his series at 700 which is why it was so rushed but you're wrong, Kaguya displayed traits and some dialogues as well as motives which was clearly havn't been answered yet but you want to jump off the fact that she has no intention. Kaguya comes as the most popular historical figure in Japan and inspired many authors to reference her by implementing into the series. Knowing Kaguya has somber backstory, she definitely gonna be realistic once that's gonna explain in the Boruto Movie, and yes I'm fan of Kaguya in general which is why I'm interested with her in many different series.
I'm one of those people who have been invested predicted kaguya to be the final villain, I took my time and research based on the philosophy and mythology and compare within the concept of this series.