In fact we have already addressed the problem. In Q3 there will be an additional page in the Update from Database wizard where you will be able to select which schemas are used in the metadata comparison. We have plans to redesign a bit more the wizard post Q3 but this should be a good start.
Another useful option that will be introduced in Q3 is the ability to update a single table from the context menu of a class on the diagram. You will get the same dialog but only the table mapped to the selected class will be checked for updates.
Hope that will help.
the Telerik team
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