Cassandra provides us with a mythological archetype.  There are many stories about the Goddess choosing a mortal male (usually a young one) and giving him special training.   Then later she might appear to him in disguise (a young female is a good one) and ask for his help.  She often gives him more help or a special token or something before the fight.  If he proves himself to be a champion (slays the dragon, defeats the enemy, whatever), then the champion is rewarded by being chosen as consort to the Goddess.  Since (in these myths), the Goddess is Immortal and the champion isn't, his position as consort is temporary. He will die, and then she will find a new consort, often the son of the old one.

The story of St. George closely follows this.  He was raised as an orphan by the Faery Queen, never knowing his true name.  He grew up, received his weapons (a sword and a white shield with a red cross on it) and wandered about for a bit.  Princess Una came along, asked for his help in defeating a dragon that was laying waste to her land.  He did so (with some magical healing from her), and then married her, becoming the prince, and the continued champion of the island.  He went off and fought more dragons and nasties, while she ruled the realm.  In the end, some versions have it, George didn't die, but eventually went back to the Faery Realm, to the shadowy land, where he met Una, now in her true guise of Faery Queen.

In Prophecy, the pattern is clearly followed.  Cassandra found the special young lad, gave him a bit of training, later asked him to fight for her and gave him some more help, then took him to her bed. (or his bed)(or the floor)(or whatever).

Having proven his worth in single combat, Duncan fights against the Horsemen (again with her there)(and perhaps her presence was necessary to help turn Methos from the Horsemen)(but that's getting into a whole new set of myths). Then Duncan is tasked with defending the entire world in the AAA arc.

Cass shows up in all three of those challenges and either helped, prodded, or reminded Duncan of some things he needed to know to get the job done. It's important to note that she plays less and less of an active role as Duncan grows in strength and self-knowledge.  Her job is to help him grow up, and then let him go (like any mother).  Some of this growth she knowingly encourages (as in Prophecy); other she seems to do unwittingly and unwillingly (as in the Horsemen episodes).

For  example: Her complete refusal to believe Methos had changed forces Duncan to take a long hard look at Methos, and (in a way) at himself. Choosing to believe in Methos is a hard decision, and Duncan makes it even with his "mother-figure" telling him it's wrong.  Duncan has grown up.  He also has grown up enough to tell her what he wants, even in the face of her disapproval. "I want him to live!"

Cassandra accepts the new adult power and knowledge of Duncan, and walks away from Methos.  In years, Duncan may be a child to her, but in that scene she acknowledges him as her equal.

In the AAA arc, her participation is limited to a reminder, a note from Mom saying, "Don't forget ..."   It's a hard road for Duncan, but he's capable of it, and she knows that.  To interfere or to offer help would be to weaken him or make him dependant at a time when he has to find the strength within himself.  Maybe Methos felt that, too, and so disappeared.

After the AAA arc and To Be and Not to Be, Duncan has finished his worldly tasks and has grown weary.  He wanders off into the mists.  We can hope he's enjoying his time of reward and rest in Tir-na-nog. Maybe he went back to Scotland, to the Highlands, and Cassandra was there waiting for him.  Who better to talk to about a demon than a witch?  Who better to ask about his dream of To Be/Not to Be than a woman who dreams of the future and has seen a heck of a lot of past?

Cassandra (like the Horsemen episodes) is fertile ground for fanfic because there are so many myths and archetypes there.

In Prophecy, she is at first goddess/witch/mother, then teacher/helper/damsel-in-distress, and finally lover.

In the Horsemen episodes, she shows up as an avenging Fury, but obviously needs help (emotionally and in the fights).  She's more of a sister than a mother, and I get no sense of a lover relationship continuing in the Horsemen episodes. There's no passion between them.  In the end, she and Duncan are equals, and the mother aspect is gone. Or, perhaps, he is her father-figure, or at least an older brother, helping her and protecting her.

(There's probably an intermediate chapter here, much wondered about by many people, where Duncan and she get together and chat a bit after all that, and get back on more friendly terms.)  (I've written my version of that meeting in my stories Kindred and Dearer Yet the Brotherhood.)

In AAA, she's hardly there at all, except in the removed wise-woman/crone guise, the words of wisdom in a dream.

I see a final chapter (not shown on the TV), where Duncan goes back to her, talks to her about Richie's death and the AAA and the NTB stuff, and she is once more mother/teacher until he heals from those wounds, and then finally, maybe she and Duncan are equals and lovers again.
 

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After writing this and corresponding with Selena about myths, I was inspired (compelled, actually) to write the story of Cassandra and Duncan after Not To Be.  That story is Changed Utterly, and it's from Duncan's point of view. Cassandra's version of what happened is found at the end of Hope Triumphant I: Healer.

All of Parda's stories can be found on her webpage at http://users.erols.com/darkpanther/.