There's quite a bit that could be added, without even touching the site's overall mechanics at all.

The markdown support is extremely minimal and doesn't support a lot of basics like quotes (which causes many people to "quote" by using a code block, which has issues).

A basic private messaging system would be really helpful in a lot of cases. Right now people always have to post email addresses publicly.

It would be nice to have some built-in visibility into things like title changes, link changes, etc. that mods do, instead of needing them to comment manually about everything they do.

They could implement some scraping to automatically add the year to older stories, instead of users needing to flag it and get the mods to do it manually all the time.

And so on.