Lately I've been using the manager obsessively and I really like the way it works, but the more I use it the clunkier the stockpile feels and I have some suggestions on improvements for both systems.
The ability to use the item type, material and trait options to define stockpiles. Both as an inclusive option to also allow all trait bearing items and an exclusive option to only allow the selected items also bearing the trait.
Right now if I want to create a stockpile for millable plants to go into my mills, there is no other way to do that than to read on the wiki to figure out which plants exactly are millable and which aren't. Some of the traits would make it really easy to select certain larger group of items such as "Cookable", "DRINK-MAT-producing", "FLUX", "Millable", or "Milk" where you either have to select or deselect a lot of items or simply have no easy way of telling from just the names and groups what to select.
There's also a few traits that I don't know how I would make stockpiles for currently. "Improvable" for encrusting and decoration, "Melt-designated", "Nearby" if it works the way I think to scoop up miscellaneous items nearby for cleaning and "Dyed" to ensure only dyed cloth and thread is used for clothesmaking.
General give/take stockpile setting
Linking stockpiles is really useful, but sometimes it would be convenient to be able to set up giver and taker stockpiles without finding each and every stockpile you want to give to of the same type where you don't need precise control of the flow of items. Setting the kitchen next to a general give stockpile will allow you to set up smaller food and drink stockpiles all around the fort as general take stockpiles to easily stock up on food where you need it. A central lumber stockpile could work the same way. Or if you want to gather up all the stone, metals and gems in different areas without having to go through a linking process every time.
It would function the same way normal links work today but with every general giver pile being linked to every general taker pile and be able to be used at the same time as the current links.
Quality and wear trait or setting in manager and stockpiles
This isn't a new suggestions but while stockpiles have a quality setting it's desperately missing from the manager for when you want to make sure you have a stock of masterwork armor and weapons at all times rather than waiting for the smelting of your current inferior stock, it can also be useful in other production where you want to ensure you have masterworks ready to be used. The wear trait will allow you to collect and dump or melt worn items. It would also ensure you don't count those worn and tattered socks laying in a refuse pile before you start making new ones through the manager.
Item recipes
I don't know how much thread I get from processing a pig tail, how much dye I get from milling a dimple cup, how much thread I can dye with a dye, how much thread I need to make cloth and how much cloth I need to make a cloak. I don't know where to find that information either when it isn't written in the wiki. Say I want to make 3 steel chainmails when I have the materials needed, when I activate the reagent/materials and products options instead of saying 10 each of everything it could say... I think it's 6 steel, 3 coal and 3 chainmails.
I know not everything is easy to tell exactly how much it'll use or produce but where applicable it'd be useful to find out in-game, especially for newer players with the steam version coming out.
Option to only count items from linked stockpiles in workshop profile work orders
When I create a job order within a workshop profile it would be really useful to have "Amount of unrotten cookable solid items available in links is at least X". Input items in giver piles and output items in taker piles.
Collapsible groups of workshop work orders
If I set up a couple of workshops to churn out and keep a couple of each clothing/armor/weapon type or something like that available I end up with pages of workshop orders in addition to everything else I order from there. It ends up being extremely cluttered and hard to find the jobs I want to look for to either check, remove or adjust. If the workshop profile orders were grouped per workshop it would be a lot easier to navigate.
Stockpile resizing
Pretty self-explanatory, I don't know if this is already part of the graphical overhaul but an easier way to resize existing piles would save on having to go through all your settings again. You could even have a move option if you end up allowing resizing of stockpiles.
Trait negation
The ability to use a trait as an exclusion. I'm not as sure of how useful this would be, but being able to exclude "improvable" or "unrotten" would have their use cases.
An example of how I would be able to set up a new kitchen with some of these changes.
Set a "take from everywhere" and "general taker" stockpile with "unrotten cookable items" next to kitchen
Link to kitchen
Kitchen profile job order, "make 1 lavish meal" with conditions
"Amount unrotten cookable items available in links is at least 30"
"Amount of unrotten prepared meals available in links is at most 60"
Link to a general giver stockpile
This would be a quicker and simplified way of setting up a kitchen in an existing supply chain that gathers all cooking ingredients from farm and butcher stockpiles, and items strewn around, ignores all the various non-cooking items in the food category, distributes the food all around the fort to garrisons, dining halls and distant workshop areas, and keep cooking until all of the taker food stockpiles are full.
Adding a new garrison food stockpile would just require setting up a new small "general taker" pile and the rest of the system would remain unaffected and not need any other changes at all.