I don't get what's so difficult and intriguing about Ungoliante and Tom Bombadil. How is there any necessity for an explanation outside of what we know for sure?
If it is this
Quote:
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The Eldar knew not whence she came; but some have said that in ages long before she descended from the darkness that lies about Arda
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that is causing problems, just remember that 1) the Atani had beliefs about their own origins that conflicted with other accounts, and possibly with actuality, so the fact that "some have said" something means very little, really; and 2) "the darkness that lies about Arda" is not outside of creation. This origin myth implies only that she entered Arda without receiving an official assignment from Iluvatar; therefore she was neither Vala nor Maia, and thus also not an Ainu. This does not mean that she was entirely unique in nature or even in circumstance, however.
As for Tom Bombadil, I see no reason for him to be anything more than a mysterious character
within Tolkien's cosmos. Apart from Tolkien revealing his real-world origins (which necessitates no special conditions for his presence in M-e--after all, Bilbo could have been based on Tolkien's uncle), why is he such an anomaly? What makes his nature so irreconcilable with the rest of Middle-earth?
Now, Beorn I really have a problem with.