We place a strong emphasis on usability and interface in crawl. For example, we actively avoid putting items in the inventory slot corresponding to using them: potions shouldn't land on 'q', food on 'e', etc. Another advantage is that we're dealing with a simpler game. Brogue takes this one step further and I think does a fabulous job. For example, there are no inventory stacks on the floor. Either there's an item or there isn't. Adding stacks would impose a complexity cost without improving gameplay.
Back in 2009-2010 on DCSS we were very fortunate to have one of our developers organized a usability study. The usability study ran over several months and produced a ton of feedback. Since the core team is around 30, we actually had the throughput to act on these recommendations.
I wrote an IRC bot last year for myself and a small community on IRC (5 of us at the time), that specifically monitored only us by paying attention to lines said in ##crawl. It also passed along commands to the appropriate bots (Henzell, Gretell, etc), and responded with their responses. The bot was pretty crappy through, as it was just an irssi script with a buncha hacked perl.
A friend in the community rewrote it as a proper bot, and has extended it much more. This little community of ours (now up to 20 or so people) has had a ton of fun thanks to this, because we get the usefulness of ##crawl without the spam.
Brogue just blows my mind with how simple it is. The magic system is reified as items. You really only have one stat (strength) IIRC. The food clock is both dead accurate and merciless [0].
I haven't played DCSS in a few years, but when I did, it was literally feast or famine: I would either be walking around with dozens of rations or else dying of hunger all the time. Herbivorous races like Spriggans didn't have very high food consumption but also didn't have many options in case they didn't find vegetarian food.
I read the summary page for the usability study, it seemed to give tons of (in particular) very _actionable_ feedback.
[0] Nethack, as much as I love it, causes brain damage in the same way that BASIC does: it shapes the way your brain works in a disadvantageous way. Consider that all of the nethack variants _add_ features (and are unabashed about it, SLASH stands for Super Lots of Added Stuff Hack).
pender has done an amazing job with Brogue. Without a doubt it's the best roguelike out there today. It doesn't have the same scale as crawl, but I think this is more of a strength than anything else. Slogging through 51 levels in a normal length game or upwards of 100 in extended is just exhausting. I joke that every time crawl gets better, we do it by cribbing something from Brogue.
Two features that come to mind are summoning mechanics and axes. Previously summoned monsters would stick around after a summoner died. This encouraged players to just run away if too many summons dropped. Instead, brogue pops all the summoned creatures as soon as you kill the summoner. This raises interesting tactical possibilities: Do I expend items to kill a summoner? Do I try to separate a summoner from other monsters?
Back in 2009-2010 on DCSS we were very fortunate to have one of our developers organized a usability study. The usability study ran over several months and produced a ton of feedback. Since the core team is around 30, we actually had the throughput to act on these recommendations.