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I’m not sure if this is a brand-spanking new feature or if I just missed it but using JetPack you can now update WordPress Plugins across all your websites through your WordPress.com My Sites Dashboard. What’s even more interesting is that you can set plugins to auto-update.

Auto-update Plugins using JetPack

Right now this feature is limited only to Plugins — no updating Themes or the base WordPress installation.WordPress already auto-update (unless disabled) so I doubt this will ever be offered. I wonder if we’ll eventually see the option of updating Themes through WordPress.com.

There are already a few services out there that’ll help you manage all your WordPress websites. Here are a few that I know of in alphabetical order:

More information can be found on the Site Management support page. And be sure to turn on the JSON API.

I can’t change anything when I try to manage my sites on WordPress.com.
You need to enable site management on your Jetpack-connected site from the dashboard by either opting in as mentioned above, or by enabling it under the JSON API settings in Jetpack → Settings → JSON API → Configure and checking the box for the “Allow remote management of themes, plugins, and WordPress via the JSON API” option and saving your changes.