I really liked the storyline. To me, the story of good vs evil, of people who want to pillage nature vs people who want to preserve nature, is iconic and powerful. Maybe Killamanjaro Safari is an oversimplified version, but then, so are many of the classic Disney movies and park attractions.
Yes, I go on KS to see the animals. And yes, I am annoyed when I get a leadfoot driver who slalloms through the course like a cop in a bad action movie, but the story line was not the source of the annoyance.
I think the story line is the main difference between KS and many of the other safari rides in the US that take you through animal habitats. The story is the Imagineers' way of "Plussing it", so that you're not just driving past animals in enclosures, you're on a real African safari, in a real nature preserve, and the story line is an integral part of the suspension of disbelief - just like the Ghost Host's narration and the hitchiking ghosts in HM (otherwise it would just be another haunted house ride), just like the Los Angeles signage and the pre-show in RnRc (otherwise it would be just another roller coaster), and just like the addition of Ellen's stuff to the Universe of Energy (without which it was just a boring documentary with nice dinosaur room).
The story lines are an important part of what makes the Disney parks so much better than any other amusement parks in the world - it's the little things, the details, the stories, and the extra steps that the Imagineers took when creating each attraction, that put them so far above the competition that they are not even in the same class.
Without that stuff, WDW would be just another amusement park.