Doesn't scale, huge load in WP Admin

Wondering how others have solved issues related to the admin, more specifically the users and usermeta related queries on the back end. As we grow with over 25,000 users, it appears that wordpress is simply unable to handle anywhere near that number of users effectively. From what I can see it has something to do with unnecessary joins caused by having user profiles existing in the usermeta table instead of being fields on the user table. If you turn on and off plugins related to a user profile, at least one mysql process results with a long query (that usually ends in a timeout), consumes a huge CPU% and load skyrockets.

I don’t have that many plugins. I have about 12, most of them off and only active in certain blogs, none of which give me trouble. Turning off every plugin doesn’t make much of a difference as it’s always the same issue. It comes down to the need to match userids on two different tables among other issues that deal with turning on and off plugins for that many users. Combine all this with capabilities and you’ve got your way for a tremendous amount of overhead just to deal with simple clerical processes.

Wondering how others might have solved this problem, if at all. At present, doesn’t look like anyone truly has.