Dynamics 365 EE removes the virtual companies functionality but offers no alternative. Cross data sharing is a replication mechanism which is reserved for group and reference data only. Currently the docs suggest that the total number of managed records should not exceed 1 million (number of records times number of legal entities) I agree that the data structure is complex but at least in AX 2012 you could try to develop such solution and limit the number of records in DB. In 365 EE the "saved data per company" property on standard tables cannot be changed. Changing the design to use a single legal entity is a solution here but it also creates other issues which I will not discuss here.
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