This is what I have drawn up for a "tech tree" sort of thing that works with the current system.
A theoretical creature (let's call it a "wingerot") wanders into the caverns and into your fortress. Your dwarves kill it, and it drops an item on death - which could be an item named a "wingerot's mechanical wing" (note that this is an item (probably a toy for technical reasons), not a body part). After obtaining five wingerot wings, you will have the required reagents for a new alchemical reaction - let's call it "wingerot research." This reaction takes the five wingerot wings and produces another otherwise unavailable item, which, for the sake of argument, I will call "advanced fabrication blueprints." This item is then used to build a new workshop, with its associated reactions.
In this way, it is possible to restrict the construction of a building until certain conditions are met - in this case, the slaying of five wingerots, though other ideas are also possible. Since the building cannot be constructed without the necessary item(s), the reactions associated with that building are "locked" until your civilization is able to finish construction. This is the essence of the "tech tree" concept using the current engine. The reactions are never actually locked, but require special materials to create the building that makes them possible. It is even possible for one of these reactions to replicate the necessary material for the building, allowing you to build as many workshop as you wish after "unlocking" one.
I am, personally, excited about the possibilities of this concept. This process could be used to justify advanced mechanics and technological advances that would break the game if available from the start of a fortress, but can genuinely enhance the experience as a fort ages. A siege could be fought off with current technologies, or weathered in hopes of a game-changing technical advancement with this system. For example, the killing of a megabeast could not only prove a historic event, but could leave behind an item that could be used to build a workshop that can fabricate a new type of weapon inspired by the beast itself. Obviously, this weapon will still be available in moods, but will not be there to create at will until the megabeast is slain and the workshop built from its unique drop. With the sheer volume of mood weapons already added, the probability of getting this specific weapon without finishing the prerequisite is both extremely low and inconsequential.
Sentinel core research uses this concept in the current mod, but produces a one-time result rather than a product that can be used for a workshop.
I would like some feedback here, as this idea may be a bit polarizing. Some people may see this idea the way I do, as potential for a deeper experience, but others may feel that the restriction on production until a condition is met is frustrating. Obviously, this is not the intention. I am a bit concerned also about the effect that adding a lot more permitted reactions and associated "technical advancement" items will have on mandates, though this should be easily averted by wisely choosing your mayor and nobility.