It also confused me that of all people, it was Jeri Taylor who thought getting rid of Kes was the best decision because as you said, she wrote stories for her in her books. Frankly I've never thought much of her as a writer and she is the one responsible for keeping those infamous Voyager holodecks just so she could have Janeway engage in her gothic holonovel.
I agree. Even if I actually like "Mosaic" and the background stories in "Pathways", I dislike Taylor's way to soothe over all problems and conflicts which were established in the series. In the series it was stated that Chakotay wasn't on good terms with his father Kolopak when Kolopak died. Taylor sooths it over by making them made up and solve their problems before Kolopak died.
The same with Torres. In "Pathways", Torres's rebellious attitude is explained by her longing for her Starfleet Officer father!
I also find Janeway a bit wimpy here and there in the background story in "Mosaic". There must have been a significant change in Janeway between the Academy and Voyager.
And we get no explanation at all to why Tom Paris had such a bad relationship to his father. It's all like "if we are a good, happy family who join hands and sing a little song, then everything will be fine". Life isn't always that easy.
Not to mention that the way Jennifer Lien was dumped wasn't particularily nice either.