I am not using all 2000 tables and 5000 procs in my project, this database is serving multiple projects. For this particular project, I am using less then 100 tables and procs.
I used preferences settings which allowed to specifically select stored procs to generate. Worked great for me. Thanks!
Just an idea to make user interface more user friendly, you can move this option to "[i]Catalog Refresh. Connect to the database.[/i]" window. I might be useful for many users.