Good questions.
Oh, there are lots of topics that still have geologists either scratching their heads or fighting over at meetings!
I've got to catch a plane in a few hours so I'll give your question its due consideration at 30,000 feet and get back to you.
The biggest question that nags me is the formation of greenstone metamorphic belts.
(https://en.wikipedia.org/wiki/Greenstone_belt)