Has it occured to you that the 3 squares a wagon needs being exactly one square more than the widest door you can make is not coincidental?
I refuse to believe that Toady's vision, for the world's most complete fantasy world simulation, does not include cities with gates wide enough to drive a cart through.
That said, I'd very much like to see building destruction tie into the systems for items taking damage, that is currently seeing expansion. DF1.0 should be a wholly unified work, and redundant code should be eschewed when practical. Treating buildings as if they were creatures, with their various construction components as body parts seems like the most obvious choice, though doing so wouldn't be as simple a change as it might seem. Plus it saves memory, and forces players to replace/repair damaged components to keep their defenses reliable (some system for automating this would be nice though i.e. mechanics carry fresh hinges to damaged doors and swap the damaged components out).
Currently, dwarven buildings are held together with abstraction, hope and dwarven elbow grease. There's no material properties for the joints, seams, or hinges of a given door. Pegs, glue, nails and fitted constructions will react differently to impact stresses, and people are going to want to see that modeled. Ideally, one would tear a statue free from it's foundation, rather than smash it to powder. (This specific example also calls up specters of statues with individual body parts and the ability to wear armor. A thought as tantalizing as it is foreboding.)
I'd like to see doors (and possibly other buildings) with optional extra components to make them stronger. This allows the ease of the current system (a door is made from a door) combined with the fun customization of adding locks and bars and custom hinges, unto the limit of the player's resources and tolerance for complexity.
The most basic feature would probably be a bar or log used to bar the door. This doesn't demand any new items to be created, and makes decent logical sense.
Another change that doesn't require a lot of new items is sandwiching doors for composite strength and features. A lightweight, compressive, wooden door might be veneered in attractive and scratch resistant granite. This opens up such possibilities as nobles with temperamental pets needing doors that are steel on the outside and their favorite stone on the inside(Fun ensues). This does require the game to recognize which side of the door is which, unless you just want to have a core and a single sheath that covers both exterior surfaces of the door.
After that things get more complicated, like with the aforementioned hinges, glues and nails.