I don't really keep track of who made what game, but my experience doesn't quite match this.
NWN2 is an ok story, with some especially weak plot justifications for the railroading, and an absolutely terrible ending. Mask of the Betrayer is a much stronger story, but I still didn't feel it had the emotional depth that NWN1 (and Hordes of the Underdark) had. Some good plot elements, but not quite on the level of Planescape: Torment.
Edit: Though, in retrospect, my feelings on MotB may have been tainted by the transition from NWN2, where I liked the story most of the way, and rather wanted to continue it rather than having pretty much all my former connections cut away in a new game.
I cannot even begin to understand how NWN1 could be said to have had "emotional depth." It was probably one of the more terrible single player experiences I've had

As for Mask of the Betrayer, I don't think it's really possible to compare Gann, or Safiya, or Kaelyn, or even grandpa bear Okku to NPCs in (almost) any other game and have them come up short. They're fully complex and 3 dimensional characters. They have their own likes, dislikes, their own tastes and desires. You don't grow closer to them by playing My First Psychologist to them or kowtowing to their every whiney demand, you do it by convincing them you're right and by making an actual and genuine bond with them.
The problem with most games is that they're stuck in "You need to save the world." It's a boring plotline - and hilariously conservative at that. The idea is that everything in the entire universe was fine and happy, and there was no strife anywhere at all, when suddenly the big bad evil guy came in and tried to alter the status quo! The hero is purely reactive.
Planescape: Torment and Mask of the Betrayer don't have that. They're both intensely personal storylines. In your standard Bioware game, you don't make any real decision. You don't change the story. The story isn't about you. You're just the pawn of fate, or the one chosen by destiny, or whatever other silly phrase you want to apply to it. You're still going to save the world at the end of the day, and it makes for a dull, shallow story. Rather, PS:T and MotB don't have you as a character in the story, but rather as the story itself. The plot literally revolves around your character. The choices you make matter a lot, often times with rewards or reprucussions far along the way.
I don't really think there's a comparison to be made. While mechanically Mask of the Betrayer wasn't the best game, it's writing carries it far above anything the Canadian doctors have ever done.