– Every table should have InsertDateTime and UpdateDateTime columns. The UpdateDateTime column should be populated with the same value as the InsertDateTime column upon creation of the row, rather than being left null.
– Whatever you use to create tables, include primary keys, foreign keys, and indexes with your table definitions. Provide explicit constraint names to simplify database comparisons. You can disable your foreign keys, but they need to be there to provide that metadata.
– Separate your final dimensional/reporting tables from audit tables and staging tables. This can be done with separate schemas or even separate databases.
People have added some more thoughts in the comments as well.