If someone could point to comments from writers from earlier in the show's run about the difficulties of writing for Kes(like for example, there WERE such difficulties with Troi in TNG season 1) then I'll drop my skepticism.
TNG staff changed their mind about casting at the last minute, too. Crosby asked to be released, but they had already been considering letting Sirtis go. Suddenly, things came to a head with McFadden vs Hurley and
she was let go instead. They beefed up possibilities for Troi for Season Two, then Sirtis lost many of those new counselling opportunities to Guinan/Goldberg. Suddenly Bev was the character "not working", and Gene Roddenberry replaced her with a feisty female analog of McCoy (ie. Pulaski), who started to nitpick at the Spock character (ie. Data).
The VOY Companion is not as comprehensive as the DS9 or TNG ones, but I'm sure there are mentions of the Kes problems there. Either there, or old "Starlog" magazines. In Australia, we had Richard Arnold as an annual convention guest, and we picked up a lot of this trivia via his presentations. He's a very good friend of Jennifer Lien, but even he shared some stories about her acute shyness when offscreen, in an effort to help fans understand what was going on, even if we weren't privy to the actual decision making process. Which really isn't any of our business, just as the McFadden Saga wasn't originally explained to the general public.
No one is claiming that Lien was a poor actress. But to infer the writers are lying when they say that her character was hard to write is unfair. Maybe the Kes stories we
did see came at great cost: in development time and staff meetings. And, in Hollywood, time is money. (Much the same as how McFadden found herself under fire during Season One because the effect of hot lighting on her hair was costing TNG time and money, with personnel sitting around while she went back to her trailer for another wash and set.)