Even if her portayal was closer to the game's she's hardly a Wily E. Coyote (sp?). Natsuki has at least a couple of "crises" so you'd have to be a little specific.
She's quite tsun-dere (though not quite in the usual sense), but she's not a lesbian in the purest sense, if that's what you were referring to. She is definetly a
Spoiler:
lolicon though, to a degree and has a
"She called me oneechan!! <3" complex
Anyway, the game portrayal may have been jarring for the mood transition and direction, but it develops Touka's character. This is an anime, not an artistic film. Mood transition and direction would be very important in the latter, but the former doesn't really have to follow those filmmaking standards anywhere close to the letter.
Utawarerumono is a work that bets big on its story and characters, so developing those characters would be paramount. It's an anime, so it doesn't have to bet big on direction and filmmaking qualities. They help, but they're not as necessary as in an art film, or even a typical film created in Hollywood.
I think you're taking Utawarerumono a bit too seriously for the wrong reasons.