I had honestly forgotten about the hooded figure by the end of the game, and I didn’t even feel particularly intrigued by it. Hell, the mystery behind the Arnassi civilization was probably more memorable to me than the hooded figure.
Just to counter you, throughout much of the game I was trying to figure out who the hooded figure was, and where he or she would tie into the game. During the final boss sequences I began to piece it together, but was still wondering when it would be more conclusive. In that regard, the extended ending was satisfying to me.
But for whatever reason, Mia decides to intrude into her daughter’s life after Naija’s already started to settle with her family. “Hi Naija! I’m Mia. I’m the mom that mind-wiped you so you’d be better at committing deicide. You’ll never guess what! I just came back from stealing the ‘Queen Bitch of the Universe’ title from Kerrigan!”
The reason seemed clear to me - she wanted Naija to experience all of the hardships that she did, and to gain the powers that she did, so that she could help Mia to dominate the surface and other worlds (and what ever else Mia may be plotting). If none of this had been set up, Naija may not have been motivated to do what she did. Her experiences shaped her. It's somewhat philosophical and true to life, in my opinion.
Mia is ridiculously off key as to what Naija’s personal values are by trying to appeal to the glory of world domination. Now I acknowledge that the game has hinted a bit to Naija’s wariness of being enchanted by power. But unless I am completely misreading her character, I honestly don’t see a significant danger of Naija somehow being tempted by the dark side. The melancholy she seems to express in empathizing with her encounter of other races indicates to me her nurturing character. The fact that Mia had to force paralyze her attests to me that she’s not interested in the power tripping business. Mia might be skilled at coercion and manipulation, but I don’t see mind control as being one of her abilities, otherwise the game would have made more sense with a zombie-Naija narrating to us from the start about the voice in her head that repeatedly tells her to “kill the Creator”.
Naija's reaction and response was completely in line with her character. While I've read a few complaints about it, I also think it was pretty realistic. The times that Naija reflected on her past and what it might have been were romantic/idealistic. Clearly she was expecting her mother to be some wonderful person. The complete 180 from expectations was a shocker. People shouting "I would have killed her right away" likely aren't considering the emotions that they would realistically feel. (That, or they have a very terrible relationship with their own parents, or they have an emotional disorder that is hopefully being treated.)
Mia is also shown to be different from Naija. She was created directly from the Creator, so it's quite believable that she has some god-like powers, herself. Maybe Naija has them (or is capable of them), maybe not - but hey, it's fiction, right? Just go with it.
I also found the idea of having memory wiped and all to be somewhat beautiful. We start off the game with the idea that we're reliving Naija's adventure through her eyes, along with her. The extended ending seems to take a step back even farther, and it seems as if the save crystals that we used so routinely were actually Naija's way of storing memories, and that Naija's son traces those memories in order to try and understand what happened so that he can find her (presumably that is his goal). It all seemed to link together so nicely, and I wasn't expecting it.
Having gone through this once, and imagining the continuation of the story, I don’t see myself developing any sort of sympathy for Mia when we bring her to heel.
So quick to judge!

I could certainly envision scenarios where I'd feel sympathy for Mia.