Pax batteries aren't manufactured to the same standards as aviation batteries. Boeing outsourced a bunch of stuff, and the quality on the batteries slipped through the cracks but presumably that is fixed now. Time will tell...if Boeing can't get it right then maybe Li batteries aren't ready for aviation yet. But it's been good since they ungrounded them.

A lot of uncharted territory technology-wise on that airplane, so there were bound to be some regulatory dust-ups. Just because the feds can't quite wrap their heads around it all doesn't mean Boeing is stoopid. I'm confident that Boeing got the design right (I know some people there), not quite as confident that the outsourced manufacturing can execute the way it's intended. But given all the new tech it hasn't been too troublesome of a new airplane other than the batteries.