Now that i see it well. it does look like the ship that crashes is the one controled by Cumberbach and not the enterprise.

I hope we get at least a season six, this series deserves an end, please Disney dont mess with the fans, finish this great series we deserve that at least. 

 The Enterprise E chasing its grandfather....thats one big ship the villian has.

 Maybe not strip it more like supress it, because we know that at the end he will get it back in order to beat the Silver Samurai. But without it he will have to use his head when he fights and not go all out berserk because he can die now and that will test his limits, facing his own mortality.

 So they take away Wolverines healing factor ??? if so he would bleed out everytime he used his claws. Still looks like he will be stuck in the middle of what appears family feuds since they have sent ninjas to kill rival familys, as we know ninjas where hired for asasinations.

 So the Enterprise is very much screwed.....the next movie we will get the NCC-1701-A

 Peper with the suit looked really cool, this suit is really nice, works apparently with mental commands.

 Those "cyborgs" are all humans injected with the Extremis nanytes, one way of replicating the super soldier formula via nanytes, so Iron Man will be going against a army of unstable Captain America. Sounds interesting.

 My guess is that Fury used Coulsons "death" to manipulate the team into action, and was saved when the paramedic got to him, remember what Stark said "he´s THE spy his secrets have secrets" Also his character is awsome and thats why they are bringing him back.

 Those soldiers the Mandaring boast may be injected with the Extremis nanites so they are in a way a army of Captain America, unstable but still very strong.