如何处理MySQL太多表的麻烦？

I'm building application where users can import their applications. For every application that user import he has option to import his users. Also, he has ability to add custom fields to the table where his users are stored. When I proposed solution that creates a new table for every users application, my chief told me that's not good solution because there will be too much tables (for 1000 applications 2000 tables). Now I'm wondering what is the optimal solution to this MySQL resource trouble? I'm building application where users can import