The reactor issue, as I remember it, was that it was boring micromanagement fiddling with building reactors in the proper order (because MC->E efficiency was not equal), and then turning them on/off as needed in the right order.
The Automated Energy Hamsters solved the on/off issue, but once it became a matter of "Push button X to optimally adjust energy!" why not just have it happen without pushing the button?
Basically, it didn't serve a lot of game purpose and it wasn't much fun, so the newer simplified version was introduced. The new version was modified again, when the 10 Matter Converters per system cap was introduced to prevent hiding all the power sources in a single, safe, system and again raise the risk of brownouts.
Metal and Crystal happened because during a long series of discussions, it came out that very few players actually gave much attention to the choice of "Crystal or Metal", especially past the first system or two captured. Again, once Metal/Crystal Converters were On/Off automated, there wasn't even that but of micromanagement to involve the player in.
There was an aborted attempt to convert Crystal to a different purpose - like being used by bigger, rarer ships more than common, low-mark units... but there was much discussion, much disagreement, and then Hacking as a Resource came along, and most people were satisfied.