What version are you updating from? The profile URL behavior hasn't changed beyond allowing for users to supply their own profile URL via the Profile URL (alias) field. Beyond that it should still have their username as the SEF alias for their profile URL. Regarding layout if you're coming from CB 1.x then it's the new canvas layout. You can check out what to expect CB to look like using our demo site below.

demo.cbdemosites.com/profiles/susan

The only reason for email address to be in the URL is because their username is their email address. Edit a user within CB > User Management and check what their Username is set to. To correct the profile layout if things have moved you can use the Canvas Layout tool within CB > Tools. If issue persists please PM backend super administrator login credentials and include a URL to a profile that's affected by your issues and will take a look.

You set the username field to not display on registration. This means the Username Fallback parameter within CB > Configuration > User Profile will take affect, which you've set to Email. This means Username at time of registration will be set to Email. CB uses Username for profile URL SEF alias. Either allow Username at time of registration, change the Username Fallback, or allow them to use the Profile URL (alias) field so they can supply their own (e.g. set to display on registration/edit and mark as required). Note this behavior was not recently implemented.