I personally feel that the black backdrop with near white content-wrapper is terrible, as a start. The old forums used a yellow parchment background which was much easier on the eyes. Think warm colors. Cool is ok, but only if you do something a bit more radical like darker background with brighter text colors.
As I've continued to use these forums, and consequently grow more accustomed to them, I still feel like making hot the default sort for newcomers is wrong, but at the same time recent REALLY needs to factor replies. I would feel much better if there was a sort option that would do that, as that just feels better to me. I want to go to the most recent post, whether that is a reply or new topic.
Hot could go on the side bar right underneath sub-communities, and you could just list the top five. Same with the newest created topics to give them visibility. Of course, keeping the side bar means you will need to allow for wider monitors to take advantage of their screen real estate, but I saw that fix is en route.
As for 3rd party stuff, riot has seemed to metaphrically straddle the fence on the issue. While some community made things are allowed, like lolreplay currently, things like FEK seem shunned. I get having a stance, but honestly this one is murky. FEK wouldn't have a reason to exist if the current forums addressed any of the concerns FEK does. I know that rioters dislikes mentioning FEK, but where exactly is the line on 3rd party stuff?
As for bookmarks and keepng up with older threads specifically, I know vbulletin has a follow thread function. Bookmarks and what have you are only used when there is no alternative, or the particular user prefers said method. The Former changes based on available features, while the later isn't likely to change at all unless your feature is TRULY more convenient than the method you compete against. Only reason I bookmark threads and replies on the vbulletin side is because google does a better job searching your forums than the forum search does, but has a pretty specific syntax and still takes advanced google skills to find what I want.
As for intuitiveness, I find that lists specifically don't feel intuitive to make. 2 spaces then enter? Even notepad handles it better.
I get that making something like this takes time, and quite a lot of it. If everything here turns out way better than competitors like vbulletin and reddit, would you release a version as open source for new upstart forum makers? Part of the reason vbulletin is so popular is that just about anyone can make a vbulletin board, so there is little learning required. If whatever this mash of influences becomes was more widespread, I doubt you would find as much resistance in the future to the unfamiliar layout.
Re:Socks - I personally nuke them and and my shoes once a week in baking soda. After you get past the white powder, it's quite nice. However, whatever solution I use has to be cheap. I consider it a side effect of really sweaty feet.