Hm, I hadn’t really thought it all the way through but let’s see:
Ibiki is definitely the Nick Fury equivalent (with Aoba and Anko as the Phil Coulson and Maria Hill equivalents).
Ino is probably the Black Widow equivalent–I’m thinking her codename is either Belladonna or Aconite or Oleander (very poisonous, but very pretty flowers).
I was actually thinking Sakura would be the Thor equivalent–in the original comics form? Where Thor-the-hero wasn’t the literal Norse god, but someone who had received Thor’s powers by being worthy of wielding Mjolnir. In this case, Sakura has received Tsunade’s powers by wielding… I don’t know, powerful gloves? (I think the Sannin are the actual ancient alien deities.)
And while RAGE!Kyuubi-fied Naruto would be an admittedly great Hulk, I was leaning more towards him being Captain America. Or… Captain Uzushio? And then have Sasuke be Winter Soldier… Sharingan Soldier? The story line for them aren’t nearly as perfect a match as Shikako as Iron Hart, but it does put Danzo in the excellent position of Hydra leader so…
I don’t think Kakashi is an Avenger. The point of it was to have the Konoha Twelve be the Avengers (and the Akatsuki be the Young Avengers/Big Hero 6), and Kakashi wouldn’t really fit that dynamic? Unless…
Is Kakashi Deadpool?
… no, wait… um… probably he’s more like Wolverine–old and immortal and tired of everything, but goddamnit he will adopt all the angry children. All of them.