certbot-auto is currently the best way to upgrade to a newer version on Ubuntu 16.04, although we’re very close to getting newer packages in their repo (see https://bugs.launchpad.net/ubuntu/+source/python-letsencrypt/+bug/1640978?comments=all).
With that said, letsencrypt in Ubuntu’s repos should still be usable and we currently recommend using it over certbot-auto. The one caveat to this is the User-Agent string of letsencrypt in Ubuntu should not be modified. It is being used by Let’s Encrypt to keep compatibility with this older client. If you’re changing your UA in the command line, configuration file, or with an external program, stopping this will solve your problem. If you need/want to modify your UA string, you should upgrade to a newer version of the client with certbot-auto.
Hope this helps!