There doesn't seem to be any reason for a changed pickup system. In DoomRL you've only every got a max of 22 items in your inventory at any time so you don't have that much room. There's no weight system, no "ascension kit", no eight-rings/amulets-of-occaisional-usefulness. You've also only ever got one item per map square, so you'll never miss a good item amongst the piles of junk. Basically, things are either very good for your build, or pointless/redundant. Plus with the time factor for pickups and the movement based dodge system (and reloads for some builds) it would make it a very dangerous.
Making an auto-pickup specific for item types is a hassle for the player (even if it could be changed on the fly), yet making it for all items is useless. The inventory and the picking of it is nice and simple currently whilst being complex enough depending on gameplay and a fundamental part your "run" or build-type/strategy in DoomRL as it is.
So, ummm, I reckon it's a bad idea....(gee I waffle on a bit)