I decided to challenge my self to making a mod that solves some of the issues. So... I decided to focus on "The late game enhancement - Mining"...
So... I created the DirtyOre mod in under 24 hours.
This mod pretty much eliminates the issue of "managing the mines".
dependencies: base >= 0.12.0
description: This mod adds 6 Technologies, 24 recipes, 12 new items, 1 new item group. This also has some background code for generating endless "dirty ore".