I would say that Nethack's are only "better thought-out", not "much better thought-out":
Nethack was my first roguelike, 20+ years ago. A year or two ago I played Brogue, and realized just how crufty Nethack is.
Let me see if I can remember all the item-specific commands, just from muscle memory. 'w' is for wielding weapons, to unwield you 'w' '-'. For armor, 'W' puts it on, 'T' takes it off. For rings/amulets, 'P' puts it on, 'R' takes it off. For missile weapons, 't' is for throw, 'f' is for fire (be sure you select something to be in your quiver with 'Q' first!). potions are quaffed with 'q', scrolls and spellbooks are read with 'r', wands are zapped with 'z', spells are cast with 'Z', food is eaten with 'e', tools (like candles etc) are applied with 'a'.
In Brogue, every kind of equipment is equipped with 'e' and removed with 'r'. Every item that has an effect is invoked with 'a'. There are no spells; instead of memorizing spells you find staves that you then 'a', and they occupy space in your inventory just like a weapon.
If you like roguelikes and haven't played Brogue, give it a shot.
Also, take a read through nethack's source and Brogue's source, and you'll see that the cleanliness of Brogue's design is reflected in its code.
It's clear you've played enough NetHack that I don't have to tell you this stuff, but for anyone who hasn't played it:
Brogue may be a lot simpler (I love both games) but NetHack lets you do tons of non standard things such as wearing a towel vs wiping your face with it vs wielding it as a weapon. You can wield rings as weapons, throw pieces of armor, dip objects into potions, engrave with wands, wield, throw, or eat cream pies... There's even a TV tropes page about it [0]!
[0] http://tvtropes.org/pmwiki/pmwiki.php/Main/DevelopersForesig...