I wonder where one can find a physics engine that can stack boxes without them flexing, wobbling and falling in a very unrealistic way [1]. It seems very common.
Well most physics engine, including nphysics, bullet, box2d, are able to achieve much more realistic simulations: just increase the number of iterations for the constraints solvers, and reduce the timesteps length. Of course this will no longer be real-time but will be suitable for generating animations. In the end, it always boils down to a compromise between performances and realism unfortunately.