* The OP doesn't own the post, the OP is just the person that started the conversation at this time. Every time I open something controversial the first/top-voted reply is a counter-point. Typically a few days later there's a full-fledged counter-point article that (again) gets voted to the top. Instead these should exists in the same space. It should be possible to replace/modify the OP or directly challenge the topic without having to start another thread entirely.
* I want to see the people I'm interested in, topics they start, and topics that interest me. My front page should be custom (and no, I don't mean reddit subscriptions). Reddit subscriptions is a manual approach to what should be a fluid-dynamic system. I might subscribe to "ham-radio" find some people I enjoy talking to and if they subscribe to something else, like "shortwave-radio", then I should start seeing things from "shortwave-radio" that -they- found interesting.
* Bikeshedding should be embraced, there should be the concept of side-conversations. It's a part of our system. The problem with bikeshedding is that it is repeated ad-nauseum and the only current approach to solve it is to delete it and push people to some 300 page/dead/closed thread from 2003. When someone starts to bikeshed, and people begin to respond, they should go into a special area that takes them away from the main group. Really what's happening is a 'side-conversation' that has it's own value to the individuals participating. It's like going to a party and discussing the merits of the Death Star, I'm sure there are wikipedia pages that could answer all questions but sometimes people enjoy debating something.
* Arguments should be embraced, and hidden. When you get into a heated argument with someone there should be a system where slowly the conversation moves away from the main thread and becomes hidden from the rest of the community. Just like bikeshedding, there's no reason to bring people that aren't interested into the conversation. Eventually these threads should be deleted, they don't need to persist forever (you can always choose to do this by taking a screenshot).
None of these are easy problems, some of them would be near impossible given current hardware.