I would find some enhancements in the possibilities for representation of air exchange helpful. It is also very likely that I have not yet figured out Honeybee possibilities. But, for the sake of discussion and continuous improvement of ladybug.tools, here my points:
To my understanding what setEPNatVent offers in terms of interzone air flow rate is not actually interzone flow with for example ZoneMixing and ZoneCrossMixing classes in EnergyPlus, but an outdoor air provided by mechanical system (at least in case of a model without air wall). Interzone mixing is, however, needed in some cases even without air wall (for example imagine the air exchange between a sunspace and another zone, which one can parametrically explore).
In the setEPZoneLoads you only offer infiltration for natural air exchange. I agree that in many cases it does not matter how we call the air that naturally comes to the building. But, firstly, it is helpful for modelers to differentiate between intentional and unintentional introduction of fresh air, but there are also cases where having both classes of natural air exchange helps (for example, to easily keep the fixed rate of uncontrollable infiltration, while doing parametric exploration of the natural ventilation).
I am aware that you offer another EnergyPlus module for estimation of ventilation (based on ASHRAE HoF). But leaving aside the uncertainties associated with that model for estimation of ventilation in dynamic simulations (which has nothing to do with Honeybee), I still find it quite useful that the modeler can explore the implications of specific air change rates in a parametric simulation, without being worried about the actual ventilation rates in the beginning.
Offering ZoneVentilation:DesignFlowRate class with all its thresholds for natural ventilation also provides the possibility to control it based on indoor environmental conditions. I saw in one of @chris videos how charmingly we can control infiltration based on the outdoor data in Honeybee. But as in case of the internal conditions, there is a feedback loop between ventilation and indoor conditions, one can benefit from the internal run-time data exchange of EnergyPlus.
I realized that setting the setEPNatVent to mode 3 results in fan-based ventilation using ZoneVentilation:DesignFlowRate. But, as far as I could say, this is always on. I think there should be a possibility to set a schedule for this.
I am not sure if there is a possibility to add specific EnergyPlus objects to the model made by Honeybee and continue with it in Honeybee to enjoy its powers in parametric environmental studies. Imagine, as an example, the zone:mixing class. One does tons of things with Honeybee. If that feature is not there yet, you just make that object in a text editor and attach it to your model.
PS: The time I spent to write such long comments just shows how much I enjoy working with your tools!