I think that part of the problem with the APIs reaching quotas is that when in the template builder, API calls are made as fast as there are changes in widgets. And let me tell you... I work fast... I can totally see how the API calls can overwhelm the system.
Why not defer automatic updates? We can just have a button somewhere that we can press to call for an update. Or even, make the choice even more seamless: have either automatic updates and button-press updates. That way clients who love it don't start hating it and clients with 500 GA accounts per template can not overwhelm the API.
Food for thought?