I guess it is a question of learning a few of the tricks. Some suggestions:
Only show direct mails in the unread folder. Hide custom folders and mailing lists.
Move important mailing lists into the important folder. Close the other folder and only click the parent folder to see what is inside.
Learn to use the view toggles. Use different settings for different folders, depending on what makes sense. I often hide unread mails to only show new ones, for example.
Use keyboard shortcuts, such as T to view a thread and E to view the contact.
Undo is your friend. If you mark a mail as read, use Undo to bring it back.
Personally I queue mails for later sending. I guess it is old school undo sending mail...
Prefetch all mails. That means all the mail gets indexed.
Search is a function you should expect to use a lot. It is fast. Thus you can spend less time organizing your mail.