Hi, chiang:
IE3D normally shouild be able to predict the real thing quite precisely. However, you need to match your model to the reality as much as possible. For example. infinite substrate model is normally very good for regular patch antennas because it does match the reality very well. For your Yagi antenna, if the substrate is not very small, the infinite substrate model still matches the near field condition very well. However, it does not match the far field very well because the major radiation is close to theta = 90 degrees. At this direction, the material in simulation is the substrate while the reality is air. That is why you can't get the pattern very well for this direction. You do need to use finite substrate model for it. Regards.