I don't think it's a flaw as much as the system is operating outside the intended design capacity. Imagine how sideways HN would go if nothing at all changed in the way the site operates, and it scaled up to 100x the userbase.
Reddit absolutely had issues in the early days (ie: violentacrez), but the issue was mostly a dogmatic concept of free speech, rather than the moderation, and manipulation now. When your subreddit's user-base in in the hundreds, or thousands, rather than millions, it's much easier to pin down bots, and bad actors.
