Lack of information & change.
That's basically what it all comes down to. There were a lot of changes in the universe between the end of the FedCom Civil War and the Republic. Herb has said a few times that the Jihad in some form had been a part of their future plans before WizKids took over, but because those future plans aren't published, the general public didn't know this and it looked like a huge change in the universe. One company FanPro was shutting down (or had shut down, I can't remember) and a new one was taking over the universe. There were new people in charge of the new company, although folks like Herb and Randall were some part of the new company. The game mechanics and the overall feel of the first few sets was much different than the games of BattleTech that most folks remembered, loved, and still played. There were new looks to some of the units, which a lot of folks didn't like (just look at the unseen issues).
And the universe was initially focused solely on the Republic. This created the avenue for a lot more bits of misinformation that seemed like more big changes to the casual observer. At the time of the HPG blackout, many members of the Republic Armed Forces break off to form their own militias, looking to seize resources and planets wherever they can, and increase their forces. These militias had allegiances to larger powers in the Inner Sphere (or a large company in the case of one faction) and were given unique names to tie themselves to these factions. Some casual observers took this as a change in those factions, that WizKids was giving up on the rest of the IS and only focusing on the Republic and these new mini-factions. The rise of these militias led to a temporary, a temporary use of industrial mechs forced into service as combat units by the militia forces and the RAF. It makes sense to those who stop and analyze it closely. At a time when there few factories and few mechs in service with the RAF, an industrial mech, even an unaltered one, can provide some benefits in combat. If nothing else, it provides one more unit for the enemy to consider & target. As time passed, and the focus shifted out from just the Republic, factories came online, mothballed units came out of storage, and the industrial units were slowly pulled from service. One more thing was the drawn down in military forces, which many thought would never happen. The Jihad devastated planets and economies across the IS as well as the military forces of those powers. When you stop to consider things, it is easy to see that the focus for most powers would be to repairing their economies and their planets, consolidating their battered military forces.
