Hi, Wavenumber:
1. What antenna is it? If it is a patch antenna with a reasonable size substrate, the radiation efficiency should normally between 50% to 90% in the resonance bandwidth. Surface wave is an important source of loss to efficiency. IE3D is normally quite accurate in predicting the radiaiton efficiency for such a case. If it is an antenna in free space or an antenna with the substrate with the same size or slighly bigger size than the patch, the radiation efficiency should be between 95% to 100%. For such a situation, you should use finite substrate modeling on IE3D in order to get accurate radiation efficiency and it is also quite accurate.
I looked at your data. It is changing much with frequency and there are many up and down's. I seldom see anything like this. I am not sure what antenna is or there are any problem in your model.
2. On IE3D, we defined two efficiency values: radiation efficiency and antenna efficiency. Radiation_Efficiency is defined as Radiated_Power / Net_Input_Power. Antenna_Efficiency is defined as Radiated_Power / Incident_Power while Net_Input_Power = Incident_Power - Reflected_Power. In some sense, the mismatch loss is included in the antenna efficiency.
Best regards.