This guy came to the same conclusion as I did, a month after I wrote mine:
THEORY: The hatred created from the Sage's decision for Younger Son as his successor gave birth to the Elder Son's SHARINGAN, or TOMOE. The "whirlpool eye" of the Elder son is the result of the Sage sealing away the Sharingan Tomoe.
The Sealed Doujutsu Theory:
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INTRODUCTION: I will start with the manga below, because it contains two important starting points:
1) "The Elder Son was born with the Sage's Eyes"
2) "The Eternal Curse of Hatred was born FROM THIS DECISION"
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1) Since it is not stated that A) the Sage was born with these "whirlpool eyes"... nor is it stated that B) the Elders Son's "whirlpool eyes" were a mutation... it is only a THEORY that the Elder Son was NOT born with the Sage's REAL eyes (Rinnegan) at birth, as stated in manga. Also, since C) this whirlpool eye is NOT a part of the evolution of the Sharigan back into the Rinnegan (S, MS, EMS, R) we cannot just assume that the Rinnegan degraded into this "whirlpool eye".
2) This point of the "Eternal Curse of Hatred" being born from the Sage's decision will be described in the manga pages below.
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We see above that the Sharingan, which is literally the birth of a TOMOE (make note of this, its important) is described as "the eye that reflects feelings", and these feelings are obviously HATRED. Furthermore, we read that "the Sharingan alligns with the person's feelings... the deeper their darkness becomes, the more POWERFUL his eyes get". The sharingan evolves from the initial one tomoe through INCREASED PAIN/HATRED.
The theory of my thread is that although he was born with the real Rinnegan, the hatred created from the Sage's decision for a successor gave birth to the Elder Son's SHARINGAN TOMOE. The Sharingan closely resembles not the Rinnegan, but the Juubi's eye itself... If we look at the images below, we can see that the Juubi itself has a Rinnegan-like red eye WITH 9 TOMOE in it. But the Sage's Rinnegan is not red and does NOT have any Tomoe...
Red Eyes, With 3 Tomoe:
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Red Eye, with 9 Tomoe:
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Purple Eyes, with No Tomoe:
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9 Tomoe, seperated from the Rinnegan circles:
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From the above images, we see that the Sharingan actually resembles the Juubi Eye, not the Sage's Rinnegan. More importantly, the last image shows the Sage wearing a coat resembling the 9 tomoe SEPERATED from the Rinnegan! It is obvious that the Sage knew or developed sealing techniques to defeat the Juubi, so it is not impossible to believe he could seal away the eyes of the Elder Son, if he indeed gave birth to the Sharingan. Especially when recognizing the whirlpool spiral IS the sign of the Uzumaki Clan (Uzumaki meaning "whirlpool"), and symbol shown on their sealing techniques:
Uzumaki Clan Spiral Symbol
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Fuuinjutsu (Sealing Technique) Spiral
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Whirlpool symbol of Naruto's Seal:
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If the sharingan tomoe are born in EVERY UCHIHA through hatred, is it not important to note Madara saying the "birth" of this curse of hatred started with the Elder Son himself...? Wouldn't this imply that he would also give birth to a sharingan tomoe (like the rest of his clan) when finding out he would not be his father's successor...?
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SUMMARY:
In ancient culture, the ELDER SON is always given the honor of "head of the family" through divine birthright.
As an Uchiha, the amount of pain experienced by the Elder Son when disgraced in this fashion would surely create enough HATE to give birth to a red eye tomoe... and the Sage, knowing the root of this tomoe (steming from the malecious Juubi chakra) would be obligated to try and seal off his son's eyes. Hence, we have the creation of the "whirlpool eye" of the Elder Son.
In conclusion, this theory is very plausable because:
1) The Sage knew sealing techniques
2) All Uchiha who have awakened the Sharingan... were born from extreme hatred
3) The Elder Son experienced the most degrading hatred in ancient culture (stripped of birthrights)
4) Red Eye Tomoe is seen in the Juubi, not Sage
5) The Elder Son is stated to have been born with the Sage's Eyes, (Sage Eyes = Rinnegan) but he is seen with WHIRLPOOL SPIRIL eyes, which happens to be the ultimate symbol of sealing techniques!
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Special Note: The POWER of the SO6P himself is said to have been created from him developing the technique of sealing the Juubi, which is the seal of the Jinchurriki....
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....and we also know that the process of USING the power of a bijuu as a perfect Jinchurriki (like Bee/Naruto) involves REMOVING ALL HATRED FROM YOUR SOUL at the Waterfall of Truth. Since all bijuu are pieces of the Juubi (Foul Chakra) itself, and described as "...Will, comprised as a mass of HATRED..." "...that connects itself to the hatred in your heart"....
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...I presume this process (removing hatred from soul) was also created/practiced by the Sage himself, which allowed him to USE the chakra of the Juubi itself (described as "Massive and FOUL") as a Perfect Jinchurriki and not be consumed by its massive hatred. Without removing all hatred from his soul, the Elder Son could be consumed by this potential foul chakra stemming from hatred... creating the beginning of the Uchiha's Curse of Hatred shared by bloodline for the entire clan.
-gHost Senju, K.U.S.H. Sage