The ending doesn't make sense? Spoilers Farseer & Tawny Man

[Witted Bastard]

Lots to respond to here. I'll pick two ideas that are on my mind:

Nor did the Fool twine in and out of Fitz' life for most of that time. In the interlude between the two series, the only contact between them was a single brief one where Fitz protects the Fool while Skill-dreaming. Fitz not only watches Molly from afar, but has Skill contact and shared dreams with their daughter Nettle.

This is a fair point. But I don't think many people would argue that the bond between Fitz and Molly is in the same league as the connection between Fitz and the Fool. Fitz is attached to the Fool cosmically. Molly is just a woman (no matter how some of us feel the power of the universe or what have you when we are in love ourselves).

I believe that the whole Fitz-Fool dynamic, besides enriching the story somewhat, is meant to address the issue of homosexuality. The reader continually questions whether the Fool is male or female. All the while we grow more and more attached to him as a character, and when we see his obvious romantic interest in Fitz we're forced to ask ourselves whether we'd be happy to see them get together. Would it be right for them to get together if the Fool is female? What if the Fool is male, would that still be okay? Ultimately the conclusion we're driven towards is that it doesn't really matter, the Fool is still the Fool regardless of physical gender. Anyone harbouring a degree of homophobia will likely have lost some of it by the end of the books. However, this philosophical journey that the reader undergoes doesn't change the fact that Fitz is straight and that he loves Molly. Fitz is ultimately able, first to acknowledge how the Fool feels for him, and eventually to fully accept it, but his own sexuality cannot change. How likely are you to switch your sexual preference if the right boy/girl comes along?

I actually think the homoeroticism is meant to make a deeper point in addition to the one about gender identity, and that is the nature of love itself. Every time Fitz blunders into some awkward statement about 'bedding with a man,' the Fool essentially asks him if a relationship can only be called LOVE if it involves somebody putting their wiener in somebody else (pardon the crudeness, I'm not nearly as facile with words as the Fool). I think calling the Fool's feelings towards Fitz 'obvious romantic interest' is actually missing the point to a degree. The word 'romance' doesn't begin to cover the depth of their relationship OR the Fool's desires for it; the idea at heart being that not only does true love not necessarily include sex, it ignores it. Fitz and the Fool share true love regardless of whether they sleep together or not, which as you say is proven time and again.