AAAAGREEED!
Roots theme has GA in there and I brought it up to them in issues or on twitter (i forget) and they couldn't see my point... refused to accept the idea that it shouldn't be in a theme.

And then things like this: https://github.com/roots/roots/pull/891

like... whatever. But agreed. GA and CPT's and metaboxes etc shouldn't ever be in a theme. Maybe theme devs will include an optional plugin that does some of that