Plugins causing thousands of tables within multisite database

Hello,

I have a multisite install that uses several of the WPMU plugins (about 20). My database is small in size, and I only have about 200 active blogs. However the database contains about 15,000 tables. This is causing timeout issues with my host WP Engine.

What are your recommendations when running a multisite install that requires this many plugins? I'm assuming I'm not the only one using several plugins, so I'm hoping there is a solution.

Thanks,
Chris