I see what you're saying. I just think, in reality, the authors and stories that are being nominated for the genre categories would probably be the same ones nominated for other categories because, in order to be the Best Whatever Genre Story, they probably have good storylines, good characters, etc.
Also, in reality, popularity does come into play when the awards are voted on, but that doesn't mean it's not based on talent. Popularity comes from widespread appeal, and in general, poorly-written stories and poor writers aren't going to have the same widespread appeal. That's not to say there aren't really good writers who fly under the radar. There are. My point is just that if they're not being nominated in the existing categories, I'm not sure they'd be nominated in other categories either.
One suggestion could be to limit the number of categories a certain author or story could be up for, but that would only be necessary if there were a problem with categories filling up, and I'm not sure that has been a real issue. I know there was a maximum of ten nominees allowed in each category, but only a few of the categories actually had ten nominees; most had less than ten. If there were other creative, talented writers who could have filled those empty slots, why weren't they nominated? It's down to the readers to nominate and vote for the authors and stories they feel are most deserving. We may only be able to vote for one, but we can nominate as many as we want, so if there was someone deserving who wasn't even nominated, then their readers dropped the ball.