A lot of the best practices for initializing/saving/restoring/etc. are handled automatically if you wrap your model in an Estimator[1] using a model_fn. It also enforces a "clean" model specification (in a new Graph) and decoupling of the input pipeline from the model.

However, Estimators are not in TensorFlow core, which means the API isn't fixed quite yet.

[1] https://www.tensorflow.org/extend/estimators