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I've read your analysis of this relationship before, and this was likely Kishi's intent. However, as a reader, I wasn't looking for an alternate identity, so the anticipation of the reveal wasn't adequately set up. For me, her character just meant another 10 chapters in what was starting to feel like a rapid succession of villains.
Kaguya had two identities which were shown : Her will Black Zetsu who was introduced by the end of Part 1 (Way before Tobi, Pain and Madara were introduced) and The Juubi which was introduced in Five Kage Summit Arc and had a lot of significance in the War Arc.
Both the Mask Characters, i.e; Black Zetsu and Juubi had a huge role in the manga; Black Zetsu manipulated all the major villains (save for Orochimaru) and The Juubi was the end goal for all the Villains (Juubi was foreshadowed in Part 1 also as Akatsuki wanted all Nine Bijuus). So, Kaguya's role in the story was already massive (Way more than all the Villains) but her contribution was hidden.
When Tobi was introduced, Obito had Zero Character or Plot Development (Except for that short Gaiden which was pretty much a short story as it was not included in the main manga), Both only happened when the mask came off. As a result, the reveal was shocking even if it got diluted (Thanks to those flashbacks). If Kishi had developed the character of Obito before the mask came off, the whole Mystery and Shock plot elements will fall flat.
The same is with Kaguya, Kishi did not show her true identity until the last moment, and both the reveals of Kaguya being Black Zetsu and the Juubi were pretty shocking (In my opinion the shock effect was more than the Tobi reveal simply because of Madara's fall).
So yeah,what you consider a fault is actually what was intended by Kishi to be considered something good. This was mostly to add mystery and shock elements.