I love Nethack, and have returned to it time and time again since the 80's. However, much as I love it, for about 6 years now I've been drawn away to Dungeon Crawl Stone Soup[1], which has in some ways evolved past Nethack. One of the main draws to DCSS for me has been its autoexplore feature, which makes exploring the dungeon much less of a chore than it was in Nethack. It also has much better use of color in text m…
Agreed about all of these except for gods. In NetHack you can't easily choose your god during the game (though you can sometimes not-easily choose your god during the game) and the difference in behavior from one god to the next is minimal. In Crawl, you can usually choose your god and thereby get different abilities, status effects, and effectively mini-conduct challenges based on what each god disapproves of. I think that's more interesting than the NetHack religion stuff, although it's true that NetHack has a slightly more complex model of gods' feelings toward you.
I've been gradually writing up a document about differences between Crawl and NetHack and I think the items behavior you mention is a huge one.
NetHack has a substantial minigame about item identification, plus various ways that items can be damaged, destroyed, or modified (beyond magical enchantment), plus ways that they can be combined with one another (including an entire "alchemy" system of mixing potions to get other potions), plus ways that one item can be turned into another item. Also, some items give status effects when carried, while others must be equipped, or applied or invoked. Also, some items have a nonintuitive or humorous use -- one of many examples is that some harmful potions can be used offensively by throwing them at monsters or by hitting the monsters with them. Monsters can also often make intelligent use of items against you.
In Crawl, every item has essentially one and only one appropriate use, and every item is immediately fully identified when used or equipped. (Item identification is still not completely trivial because some items are harmful to use, or are consumed by use, so you might not want to use everything you find.) Items can never be permanently changed¹ except by enchantment or curses, and items can't be damaged, nor can they be destroyed except by using them up or dropping them into deep water or lava. Also, monsters make comparatively minimal use of items and don't pick them up.
You can see where various people might prefer one style or the other!
¹ The one counterexample I can think of is the dragon-slaying lance that becomes more powerful every time it kills a dragon.