So, there's going to be a movie coming up, like you said, about government-registering superheroes or whatever.
Definitely part of that is going to be stuff that you mentioned. "These guys all seem kind of similar, they all destroy a lot of stuff, they have similar origins, they could be anybody."
Avengers 1 was much more clear-cut. Aliens invading, go stop them.
Avengers 2 was almost entirely stopping a threat that they themselves created (either Ultron or Hulk).
Avengers 2 also had some overtones of "the common people are mad/angry at the Avengers"- check out the reaction to the "Iron Legion," Stark's little toy robots with loudspeakers.
There's also the matter of Scarlet Witch basically mind controlling a city into evacuating.
So yeah, they're definitely trying to set up a "There are legitimate fears of superpowered people," although I don't know if they'll be able to do a better job than the Justice League cartoon did.