Personally speaking, the best place that I've worked at that mostly solved that balance, was Pivotal Labs. Technically, it was Cloud Foundry, but same people. The way they use Pivotal Tracker and the process around it was mind blowing. Unfortunately, it is really one of those things that you can't just read about and understand. You really had to be part of their culture. It was a cross between cultish and military precision. You can google around and read up on many blog posts. The PT documentation [0] spells a bit of it out too. It was intense, but I really enjoyed my time there.
[0] https://www.pivotaltracker.com/help/articles/gettingmore_int...