The system doesn't have flaws since its creation, but the flaws have been created after the implementation of the system, IMO.

I don't feel that the reason for quality posts to be missed is that people mostly Merit the posts that they agree with, but the reason behind that is the excessive spam that is posted after them, and no one with the right mind would dig deep in that shit only in the hope of finding a quality post to Merit it. I don't see any reason to blame the system for that.

On the other hand, those abusers would not leave any system to be flawless at all. They will play their part in ruining it completely, but fortunately, they only partly succeed in that. Have a look at the trust system. Even though it makes no sense for them to leave a trust on a profile since it doesn't make a difference, but they do abuse it by spamming people's profiles only because the system hits them hard in the face. But I think it is serving its purpose, as well as the Merit system, no matter how people try to turn them negative and use them the other way, they would still keep doing their work, to some extent.