We support 2 step authentication via app specific passwords, but unless the user knows that, the process is very confusing.
Login to WordPress.com using regular password:

If you login to a self-hosted, the Jetpack screen accepts the master password initially, but then stats don't work and further Jetpack screens won't accept the password:

We support 2 step authentication via app specific passwords, but unless the user knows that, the process is very confusing.
Login to WordPress.com using regular password:

If you login to a self-hosted, the Jetpack screen accepts the master password initially, but then stats don't work and further Jetpack screens won't accept the password:
