Currently DF has two very different mechanics in place, one for making workshops which are almost all 3x3 pre-defined objects and another that lets flexible sized 'rooms' be created from a piece of furniture that has been placed. I find the room system to be more interesting as the player has far more freedom in shaping and sizing while introducing the valuation system which is fun to experiment with trying to constantly 'out do your self'. In the interests of simplicity (in terms of the number of systems that must be learned to play the game) I propose that the workshops be defined in the same manor, from a piece of furniture and then requiring several additional items to complete. A minimum number of tiles could be required for each shop and this could vary more then it currently dose as we break out of the everything is square mentality. Any floor space above the minimum contributes to additional capacity for the workshop meaning it can hold more before becoming cluttered. In addition if the room encompasses more then one of the defining pieces of furniture and the player can supply the additional components in multiples and space is sufficient a workshop can be defined as a double/triple etc etc workshop and will be able to hold that many dwarfs simultaneously working on multiple items of the single build queue.
I've brainstormed a few additional furniture pieces that would be necessary to implement this, in general I'd try to keep the number to a minimum and re-use existing items as much as possible. Here they are listed by the defining furniture.
Millstone/Quern - (I don't really see the point of making Millstones and Querns being different, I see them as interchangeable)
Mill, Quern, Jeweler, (Potter if ever implemented, also needs Oven)
Oven - The oven must be made of stone and might be built on sight rather then being placed as furniture:
Kitchen (also needs Table), Wood Furnace, Smelter, Glass Furnace, Kiln, Forge, Ashery, (Potter if ever implemented, also needs Millstone)
Table - Defines many workshops as its fairly generic and used in practically everything:
Kitchen (also needs Oven), Alchemist (also needs Chest), Butcher, Clothier (also needs Cabinet), Leather works, Crafts Dwarf (needs 2 tables), Alchemist (also needs Chest)
Loom - A specialty wood only furniture piece used only for you guessed it the Loom
Frame - A frame is just set of wood or metal pieces of various sizes and shapes that allow other things to be set at right angles and joined together or worked upon, you will need to bring this with you in the wagon like you must bring an anvil because its made at the carpenters shop but it would be cheap! : Carpenter, Bowyer, Tanner, Siege Workshop (needs 2 Frames), Mechanic
Cabinet - Normally stores cloths so is used to store finished clothing from Clothier (also needs table)
Bag - Normally used in processing Plants to Bags hence defines a Farmers workshop
Chest - Used to store the various vials that the Alchemist uses (also needs table)
Cage - Used to hold Animals hence defines a Kennel (needs 3 Cages)
In addition to these furniture items their would likely be a usual sets of buckets, barrels, Anvils, Vials and generic building materials currently needed to create the buildings, I've merely focused on the key furnitures. In fact and I'd be in favor of increasing the amount of these non-furniture items necessary to create the workshop along with some more workshop specific tools which need to be brought on the wagon or traded for (but again like the frame they should be CHEAP not god-awful expensive like the Anvil). For example a "Saw" being used to make the Carpenters shop as well.