Being a new Urban Planner that did a senior paper on using games to help plan cities, it's nice to know that others are thinking along the same lines (Especially someone as awesome as Notch!) I know gamification is considered by some to be a dirty word (I go back and forth about it myself...) but I think that using interactive digital worlds is going to happen more and more to help solve real-world problems. Whether they are "gamified" or not, I do feel that the "Virtual" and "Real" worlds are going to come closer and closer together, and video games help teach us how to interact with the Virtual.
Cash-strapped cities like the one I work for tend to use Google Sketchup to model cities on the cheap, but even that program has a steep learning curve for people not used to working in 3D. Minecraft is a great way to bridge the gap between maneuvering in a 3D digital world (what we do in games) and creating in a 3D digital world (3D modeling), as it gets people to truly think three dimensionally on a 2D screen. Until holograms become commonplace, bridging that gap is extremely important for working with visualization tools, and visualization is key to creating better cities.
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R, I'm tired, yet this idea excites me!