I have two ATSF and two CNW RS1's from Atlas. I considered the MTH, but was after the details. Atlas had road number-specific details such as steam generators while the MTH were more generic. As to operating systems, I have sometimes considered switching my Atlas units over to Proto-2, but it hasn't really been worth the cost/effort up to this point.
The "ScaleKing" MTH units definitely give you more bang for the buck, though as if I had to do it over again, I couldn't justify the extra $175 for the detail of the Atlas unit over the MTH, especially since Mario now has pilot spacers for RS1's.