Yes. The old aliens were only controlled exosuits. CONTROLLED does not mean they are in it. That would make sense because first, the aliesn dont fit in the troopers, scouts or even the hunter. Second, that's the reason why the scouts have to recharge. When you enter the alien ship in Crysis, you see a scout beeing recharged or something that is exactly the same. Now they fight personally. You can see organic parts on the new aliens, wich the old ones didn't had.
Guess for the legs: They can only fly in a certain area around a mothership, or their homeworld. That the Scouts have to recharge is another possible proof. Now they have built legs to move around on the earth, while beeing independant to a mothership and to fight in an urban area. You CAN find similarities. The aliens in the mothership had those dreadlock/tentacles at their back, wich the new ones have, too.
The Blue machine things are only machines, and not aliens. But they are controlled by them. When you stand near a Hunter in Crysis, you can hear the mechanicle movement of certain parts of the legs. And the material doesn't have to be steel. We're dealing with aliens here, maybe they have their own material for armor.
EDIT: You have to look at the aliens as a species, not as all lool a like aliens. Like we have different Skin colours, they may have different armor and skin colours. In Crysis the naked aliens were blue, so were their suits. In Crysis 2 the aliens are Red, so is their equipment. It makes sense, you just have to look closer.