I've had this idea for a story hook for a more spirit centered game, but I haven't yet been able to put it to fruition. Maybe you can put it to some use here.
The basic idea is this: A wizard on the white council had a wife, they were happy, she got pregnant, she was hit by a car. She didn't make it and the wizard, devastated by this, turns to necromancy to keep his wife's body alive. The child is born, but the council gets wind of what's going on and kills the wizard. The girl, now orphaned is put into foster care. A few years later, say around the age we first see Ivy, she suddenly falls into a coma without warning. She just collapses and nobody knows why. Her body is kept alive in a hospital, but her spirit is floating around the city, more or less thinking she is dreaming. Due to her circumstances, she's got tremendous natural power over ghosts, and if she's close, anything dying creates a spirit that sort of follows her around. Which doesn't go too well for regular folk, if she's looking for her "kitty", and it turns out it's the mad spirit of the tiger that just died in the local zoo.
If the players find her, she could become quite a powerful and important ally to them in locating the spiritmancer.
What sort of clues could I feed to my players without going all deus ex machina (they can be sometimes a bit oblivious)?
Players usually are. And I'm saying that both from a player and a GM standpoint. As a player, I feel incredibly daft a lot of the time. Then again, as a GM, you know all those little connections and tend to overlook the things that are important to actually be able to get something.
That being said, the important thing to know here would be: what are your player characters? That could be important when it comes to the kinds of clues you can put in.
What would make an interesting finale, other than the classical Meet Evil & Fight Until She Dies?
How would a strong spiritmancer defend herself, or what kind of defences in general (like wards etc)?
Now when I think spiritmancer, I think ghosts, I think memories, I think soulgazes. One of the things I would have the spiritmancer have available as a defense would be some pretty nasty ghosts. I mean make Freddy Krueger flinch nasty. And then I'd send them inside the characters minds, forcing a soulgaze with that spirit onto them. They would basically be sucked into the spirits memories and be trapped in them, until they find their way out of it. You can do that a few times, as long as those spiritscapes are different enough. Though more than 3 times is probably going to become boring. You don't need any extra rules, either. Just treat everything as if it was reality. It's especially nasty if wounds translate to the real world.
If you have one of your players who you know can pull it off and would like it, have their character possessed by a spirit and let them act against the group. Nothing like a good exorcism to add in some nice drama.
After a buildup with these kinds of things, you can easily have the fight against the spiritmancer be fairly anticlimactic. In the physical realm, her powers are useless.
What sort of novel applications for spiritmancy are there?
Well, some applications are described above. I would probably have her set up everything in advance, since the real powerful stuff just takes time. And she's probably not too kindly to spirits, so they won't just work for her unless bullied into it.
Now if you want to have a bit of a freaky fight in the end, how about this: She's bound tons of ghosts to her stronghold. But not in one piece, she's ripped them to shreds, small enough to not have any individuality but big enough to hold a lot of power. She's got so many of them there, that the nevernever is bleeding into reality. She's basically got the "demesne" power in that place, because she controls those ghosts, so she controls the nevernever that bleeds over. I would probably have her pull from the former ghosts' demesnes, just to have a theme going through, but anything is doable here, really.
