Didn't read the entire thread but... here's what I think.
Standardized control in roguelikes would be ideal, but as stated before, it's not very likely to actually happen.
So, for this reason, we should be thinking outside the box. A few roguelikes currently support remapping the controls to (almost) whatever the player wishes. This is good practice imho. However, the problem is, remapping the controls usually involves editing (or creating) a file and swapping controls around until you find a configuration the game likes(eg. No key is mapped out to more then 1 command). In addition to being tedious and frustrating, its also not a very good solution.
I don't know if most roguelike devs are just too busy or just don't know how handle file i/o, but it appears to me that allowing the player to remap the keys from in-game is not only the obvious solution, but trivial to implement as well. Upon exiting the options screen, it merely has to save the keymappings (along with any other options) to a config file. Problem solved. Everyone wins!
Although, I do not think that standardized control are THAT important, it certainly would be nice if I could just load up the game and get started without getting bogged down by help files. For this reason, I deem movement controls to be the most important. There seems to be a huge split in the roguelike community about numpad vs hjklyubn vs arrow keys. The easy solution is, support all 3! It's not that hard. Seriously.
Other then movement controls, I rarely find myself being annoyed at the controls chosen for any given roguelike. However, inventory management generally seems to be more complex then is necessary. Have any of you played Astral Tower?
http://lordarchibald.republika.pl/main.html Although a very incomplete game, he had the right idea as far as inventory goes(Although I admit I think he OVER-simplified it). An more specific example of why I think inventory management is Nethack.
Observe the following Nethack commands:
(P)ut on
(W)ear
(w)ield
(R)emove
(T)ake off
They all do different things(technically), but they also could be reduced to a single command. Even commands like quaff, read, zap, etc could also be simplified down to the same command easily enough. If there is a legit reason to make it a separate command, then don't hesitate to do so.. but don't make it it's own command just because you can.
Anyways, that was just my 2 cents...