Sorry beforehand for the long post....
1: Without a doubt, Obito is the only one who should have been the final villain. He's the ultimate representation of what Naruto would have become if he turned bad, he is responsible for all the hardships our 3 main characters (Naruto, Sasuke, Kakashi) faced, he was the true leader of Akatsuki who've been the main opponents since Shippuden began, he was an epic chessmaster who played the entire ninja world like puppets, he had very strong characterisation, we've known of his legacy since near the beginning (due to Kakashi's guilt), he recreated the Juubi and was the 1st shinobi since SO6P to become its Jin, and one of Naruto's main themes, 'the younger generation will always surpass the previous one', would have gotten very good representation because he, the new gen of evil, would have surpassed the past gen of evil in Madara if he had become the final villain.
For these reasons, no one other than Obito should have been the Final Villain. But, if I was to compromise and agree to a less than proper Naruto ending, these were the next best choices:
2: Madara - He came up with the Moon's Eye Plan, was the oldest villain we knew of (until the Kaguya stuff), was extremely powerful, and the whole 'Yin and Yang (Naruto and Sasuke) vs the New Sage (Madara)' would have been an appropriately epic and meaningful final fight. Though he suffers from his lack of connection to the main cast in the backstory, besides being an ancestor of Sasuke. If he had been final villain though, he should have gotten a different power-up (such as Shinju's Fruit) than 3rd Juubi Jin, or preferably Obito never became Juubi Jin.
3/4: Sasuke - He's been Naruto's rival since the start and one of the series' main plotlines has been his character development. A final fight between him and Naruto would have a lot of emotional investment. It also represents again the whole 'new generation will always surpass the previous one' theme and parallels the end of Part 1, Hashirama vs Madara, and Ashura vs Indra.
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But as I discuss in the link above, he didn't shape the backstory and lacked the suitable power (and I don't know, him being the 2nd Juubi Jin after SO60P wouldn't have worked for me, I've always felt the last Naruto vs Sasuke has to have Sasuke at the peak of his own natural progression, not with something like the Juubi sealed inside him). Tied with the Juubi in suitability.
3/4: Juubi - It was the starting point of all the negative power in the series. But, it's just a beast, a force of nature. It wouldn't have worked as well as Obito and Madara for me, who are actually strong-minded men and shaped the backstory. Tied with Sasuke in suitability.
5: Kabuto - It would have had the nostalgia of Orochimaru but without the crappy sucking-up Orochimaru (who was left behind long ago) as final villain would have had. Plus, the whole 'new generation will always surpass the previous generation' theme yet again. Like Sasuke though, he suffers from not enough influence in the backstory.
Kaguya genuinely is the worst choice. She has no connection to the main cast and she has no longstanding presence in the series (we only heard about her just over 20 chapters ago). There's absolutely no emotional aspect to a conflict with her.....
Sorry again for the long post
