Yes, everything is now submitted electronically. The advantage to this is that you get to keep all your original documents including your BRP and passport during the period your application is being processed .
There are no longer same day in person decisions but there is a super priority option whereby you pay an extra £800 to get a decision within 24 hours. From reading posts on a couple of forums, this is now working quite efficiently.
Even though you keep your passport, you cannot travel while your application is being processed, so paying for super priority is still an advantage.
If your wife entered on a spousal visa, she can submit her application within 28 days before her 30 month anniversary from her date of entry into the UK or at any time after that before her current visa expires. If she came in on a fiancé visa, her application can be submitted within 28 days of the expiry of her current visa. (Confirmation needed on this, please! )
When her application has been submitted, she will be directed to the Sopra Steria site to make an appointment for her biometrics to be enrolled. Her supporting documents should be uploaded before the date of appointment unless she is having them scanned and uploaded at the Sopra Steria Centre. Originals of uploaded documents should be taken to her appointment.