Can EnergyPlus fully replace WUFI for thermal behaviour simulations?

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If by "whole building simulation" you mean annual energy performance of the HVAC and other systems serving the building, then EnergyPlus may be the only choice. WUFI is probably better for a study focused mainly on moisture performance of the envelope. The model in EnergyPlus was similiar to 1-D WUFI at the time HAMT was added. Because of a lack of input data for materials, HAMT has not really been used all that much and it should be used with caution and probably checked against WUFI.

My understanding of WUFI is that it can model 1-D and 2-D heat transfer with detailed moisture (hygrothermal) modeling.

Surface heat transfer in EnergyPlus is 1-D transient with limited moisture modeling capabilities which should give similar results to a 1-D WUFI heat transfer model (no moisture).