The hassle could also be lessened if we could save custom stockpile setups, so we'd only have to go through it once.
You could do this now with the macro recorder, but it's not ideal. But you could save up the macros you created just in case Toady implements saving custom stockpiles, then convert them.
The only problem would be if categories changed, you might have to recreate a lot of macros.
Actual i might look at this, if it goes :-
goblin fat
goblin tallow
gremlin fat
gremlin tallow
etc
Macros would be the way to go
EDIT : I tested this AND IT WORKS (you only have to do the hard bits once ever if you keep the macro).
EDIT : steps below work, but there was something called 'fluffy wambler pudge' in the middle which meant the fat/tallow pattern wasn't 100% reliable. All up I had every fat selected and no tallow in under 2 mins.
Steps to reproduce
1. hit 'p' then 'f' then create a stockpile hit 'q', cursor over stockpile, and hit 's', navigate to food and 'b' to block all. navigate to 'fat' section, put cursor on first fat OR tallow, depending on need.
2. hit 'ctrl-r' to start recording, take it slow now because every key is recorded. If you make a mistake hit 'ctrl-r', move cursor to next unselected item and use that as the start for the page. Hit ctrl-r to start a fresh recording.
3. select every alternating fat or tallow, your choice. Try and swipe several pages, I did one page only and regretted it. make sure it's on an UNSELECTED fat or tallow (matching your needs again) before hitting 'ctrl-r' to stop recording then 'ctrl-s' to save. It'll ask for a name.
4. Now, hit ctrl-p and it'll swipe as many pages as needed. Make sure it's finished moving before each click on ctrl-p, you need to check it's swiping the right ones as you go because the pattern isn't 100% reliable (fluffy wambler pudge), or if you hit ctrl-p or any other key while the macro is still running it might interfere.
I Use this method for selecting trade goods too. ctrl-l lets you load a macro.
You only have to do this once, after the macro is working it can be used to create the opposite type of stockpile with less work (steps 1 and 4 only).