Dungeon Crawl Stone Soup is indeed a brilliant game. Some of the best gameplay I have ever experienced in any game, commercial or not. And it's interesting how this happened by organic iterative design with a few guiding hands over years, rather than the typical commercial big bang release date with years of up front dev.
DCSS does suffer from the optimum local minima thing as well, though. There are a lot of big design choices that stick around because they've always been there, rather than being good choices. For instance: the difficulty curve, melee being superior to spell casting, big random damage spikes, length of the game (too long), tediousness of summons / spell casting, kiting as the optimal strategy 99% of the time, and the other things that make dcss what it is.
I agree with some of the sub-optimal design choices you've mentioned, but I think the Crawl team has shown itself willing to be quite able to change the game to reduce tedium, even sometimes when a lot of players express reservations. For example, in terms of game length, Orcish mines has been reduced to 2 floors (used to be 5), Swamp/Shoal and Spider Nest/Snake Pit have been reduced to 4 floors (used to be 7), The Vaults have been reduced to 5 floors (used to be 8), the Dungeon has been split into Dungeon (15 floors) and the Depths (5 floors), rather than the old 27 floors. The weight limit for players that required low-strength casters to juggle items is gone, removing an important source of tedium.
I'll say this: I've played both NetHack and Crawl (and many other roguelikes) and the main difference between the two of them, for me, is that I have fun playing Crawl and I have never enjoyed myself playing NetHack.
One of the fantastic design choices in crawl (actually true for netball, too) is that it isn't balanced across all race+class combinations. Some are easy (mainly hack and slash power combos, like the gargoyle fighter) others are tough but trash you a lot about the game (tengu conjurer), and others are nigh impossible (mummy almost anything). If something is to easy, you can just choose to play a harder game, with less tolerance for mistakes. Eventually you start finding mistakes you weren't even aware of...
DCSS does suffer from the optimum local minima thing as well, though. There are a lot of big design choices that stick around because they've always been there, rather than being good choices. For instance: the difficulty curve, melee being superior to spell casting, big random damage spikes, length of the game (too long), tediousness of summons / spell casting, kiting as the optimal strategy 99% of the time, and the other things that make dcss what it is.