Kobato didn't show up in the game much either until the final route. There's not much difference between how much she appears in the game vs. the anime. In fact you could say that she's had just as much time in the anime as she did in the game, despite the anime being much shorter, thus you could say they technically increased her screen time overall.
That's why she's not popular. Basically, it's REQUIRED that you play through Takashi, Shuusuke, and Hayato's routes before you do the final route with Kobato and she gets any real development, and by that time, the characters that you like are already kind of set in stone.
IMO, anyway. But I imagine with her low popularity that it's an opinion shared by many though. Plus she doesn't really have much going for her other than being cute(not that it's a bad thing!)
Personally, I'm a Naru man!