There is a separate thread that addresses the differences in simulation speed between DOE-2 and EnergyPlus. Some of that information--including the speed difference itself--is relevant here. If you need results very quickly, you should probably use DOE-2!
More to the point of the question, there is a simulation capability gap between DOE-2 and EnergyPlus. EnergyPlus does a more realistic job modeling radiant effects, and unmet loads, and novel systems, and controls, and some other things too. If these effects are important in your design then you probably want to use EnergyPlus or something similarly capable. If they are not important, then it doesn't matter which you use and you should probably use the one you are more familiar and productive with. Or DOE-2 if simulation speed is very important to you.
How do you know whether "EnergyPlus capabilities" are important in your design? That is the rub. I believe California is developing some design-feature specific guidance on tool use (e.g., if you are modeling natural ventilation please use engine A or B, otherwise use A, B, C or D) although I don't have a reference for that (I will try to find it and then edit the response). The ASHRAE 140 tests can be used in a similar fashion although they are not very accessible for this purpose. We certainly need to develop better guidance in this area.