Couple things. The first isn't just about Karpyshyn ignoring the lore, since after Bane I don't really take much of what he writes as Canon, Bioware did the same thing. If you watch the Histories that they did again, they kind of go out of their way to completely ignore most of KotOR 2 like it never happened. Kreia's lore regarding Revan and all that doesn't seem to be mentioned, the eradication of Malachor V due to the Mass Shadow Generator, the second Civil War. It's just not there. They seem to have only really kept The Exile and given her a name. Talking with my friend about Meetra after the Revan book came out, we both had the same conclusion: Meetra didn't feel like the Exile from the game. They also played around a bit with Naga Sadow's history from the original Tales of the Jedi comics.
The second is about Nihilus' power. It wasn't just his tunnel vision on a planet that was his weakness, it was his need to consume that was his ultimate downfall. Kreia says that he is a wound in the Force, much like the Exile is, only this wound consumes and destroys endlessly. He is Lord of Hunger for a reason, he needs to feast on the Force and the beings of the Galaxy. In the end, he would have consumed all life and then starved to death, eating away at his own essence until he was nothing. This is evidenced by Katarr, he consumed the entire planet, with the exception of Visas.
Ignoring KOTOR IIs lore was most likely intentional. Bioware didn't make KOTOR II and it seems like they go out of their way to avoid acknowledging it. Notice how much more emphasis they put on the first KOTOR which, while it was an amazing game, was not nearly as popular as KOTOR II? They didn't write KOTOR II so they want nothing to do with it. That's it in a nutshell, and it's pathetic.
It isn't just something they should of skimmed over, considering she rebuilt the jedi counsel.
I also agree that the Meetra we got in game doesn't feel like the Exile at all. I don't even remember having the option to act all psuedo mystical ******** in KOTOR II, let alone every line she said. Also they put way too much effort in to basically making her Revan's *****.