As for the Clan encounters, I hope they aren't controlled by players, it would allow the developers to make battles against them much more interesting. I don't know who would pilot them though if they aren't players. The one thing I really do hope they keep is the complete asymmetry that existed between Clan and Inner Sphere designs. Clan stuff was way better than the IS equipment. I think it would be awesome if however the Clan battles are set up, they are set up in such a way that the Clan mechs are always outnumbered because of their superior equipment. Making them more like boss battles.
This all falls apart when (if?) players can pilot/salvage Clan stuff though, so I really don't have any good ideas. End game I bet everyone will have Clan mechs fully kitted with Clan equipment, completely locking out any lesser mercenary corps in the same way World of Tanks clans are dominated by T9 and T10 equipment.
I honestly don't know what to expect when it comes to Clan equipment. Whatever they do I just hope they do it in such a way that doesn't create massive gaps in "power level" between long time players and newer players.