Consider the fact that many, many programmers frequent LW. It's quite likely the majority of members know how to program a computer, and most of them have a very high level of skill. Despite this, contributions to LW's codebase have been minimal over the life of this website. I take this as extremely strong evidence that the friction to getting any change through is very, very high.
I don't want to propose any solutions because I don't understand what the source of the friction truly is. If you understand the real sources of friction, could you explain it in some more depth?
I sense that the lack of contribution to the codebase is because it's inconvenient, not necessarily difficult. It seems that it's inconvenient for the reasons you said: 1) the reddit fork is hard to modify and 2) the site owners are reluctant to change.
But I also sense that the proposed features aren't too difficult to implement (because they're relatively common) ...
I think it'd be a good idea to keep a list of the ways we'd like to see LessWrong improve, sorted by popularity. Ie. email alerts for new responses.
So if you have an idea for how LessWrong could be better, post it in the comments. As people up/downvote, we'll get a sense for what the consensus opinions are.
I think there's a pretty good amount to be gained by improving LessWrong.
Note: I say "ways to improve" instead of "features" because "ways to improve" is more general.