I feel like there’s a bit of cart-before-the-horse thinking here; as you acknowledge, a lot of it is organic. What makes a social site like this is the people, and specifically, the dynamic/active people who become the hubs of content or who are known characters - for instance, shittymorph (with their incredible talent for weaving fabrications before the inevitable twist) or poem_for_your_sprog who had a natural flair for both poetry and snark. Without individuals with personality, a place just becomes a noticeboard for the posting of memes or information, driven by algorithmic calculation rather than human spark. The downside is that one can never really create such a place from the ground up (hence the collapse of GooglePlus). It emerges over time from the cascading actions and interactions of diverse individuals who come and go over time.
We can certainly set standards and rules and metrics, but to actually ensure community survives and flourishes is an unknowable alchemy. Anyone can say “this will be our official meme format”, but whether it takes off or is replaced by one throwaway line from a random person can only be known after the fact. All we can really do is post and interact and try to be the people who would live in a constructive community.
The problem is one of those evolutionary arms races, for a reason in your observation: if the points are useful in seeing the popularity of a given post or comment, then why not simply create a bunch of fake accounts to boost said post/comment (which is exactly what the OP was complaining about in the first place).
Individual karma ratings allow a weighting for upvotes so that, in theory, contributors who have a track record of constructive interaction can be the ones who have more influence on what rises to algorithmic prominence. But, of course, everything can be gamed, hence upvoting bot/sock puppet-rings like the one OP observed, or people buying accounts on reddit that had pre-established karma to let them astroturf away with impunity.
No idea what the long-term solution is, beyond the vague “build a community of known faces/names” which runs the opposite risk of turning cliquish or closed-off to new content. Or maybe abolishing all algorithms and just sorting everything by new (which brings us back to the ancient commenting issue of a whole chain of people saying “first!” rather than adding any meaningful observations).