The main innovations are:

Transport multimodality. It handles multimodal transport networks: roads, railways, waterways, and maritime.
Administrative units. The data are structured using the country's appropriate administrative level. There is no need to define the origin-destination point; the model handles it automatically.
Supply data. The model directly ingests economically-meaningful data that represents the size of a sector in one admin unit.
Other noteworthy changes:

There is now one household per admin unit instead of one representative household for the whole country
For some flows, agents can probabilistically decide between different transport modes
Changes in the model structures:

the ability to handle multiple sets of input files
parameters are set aside and more easily manageable