Yes, this exactly. a door is not the same size as a rock.
Personally I like the Diablo/resident evil 4 style of inventory where everything is a certain shape and inventory management is a puzzle in itself to fit more in. That coupled with weight has always been my favorite.
EDIT
I think stacksize is also important, limiting the itemstack size is a clever way to implement limitations in Minecraft for larger objects and should be carried over.