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KrakHed
Your tangent about Thrall is actually pretty appropriate, because it hits on the other overarching issue with Aggra, and that is that outside of Thrall she's a nobody. This isn't necessarily bad, but even the token orc wife traits are just there to enable him to get hitched. Being a satellite character is sometimes fine and that's why I'd emphasize her as representing Thrall's messiah complex, obligation towards the orcs and such, with whom he parts ways while recomitting himself to a different path.
The issue you run into with your Outland idea is that Jorin is far more suited for this, because for Aggra you'd be working with a blank slate. She's a strange character in the sense that she's a Mag'har pretty much solely in that she's spiritual, but she runs counter to both AU and MU in her lack of militancy and attitude towards the Horde. Jorin already represents a more measured warrior archetype than Garrosh as well as a leader figure. Aggra replacing Geyah as a spiritual center might work, but I'd still emphasize Deadeye's son if we'd be doing this. The MU and AU Mag'har meeting up and clashing would also be fun so no argument there.
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Skytotem
You're right, which is why I'd mostly use her to get Thrall out of his funk. She'd have points to make sure but she'd largely be meant to be wrong and much like she induced Go'el onto him, he'd go past that into just wanting to do some good for his people, without needing to be their eternal babysitter, imposing values on them or what have you.