For Iron Man 3, the ending with the Clean Slate protocol marked the ending of Tony's overall character arch. To me, looking at all three Iron Man films, Tony became Iron Man as a means of atoning for being a war monger, but to deal with his insecurities about his life, that he never really accomplished anything truly worthy, unlike his father. In Part 2, it deal with Tony trying to come to terms about being Iron Man in addition to dealing with his disconnection he had with his father in the later years. When it came to Part 3, I had the feeling that when it comes to the Iron Man suits, they were a crutch to Tony as a means of dealing with his psychological problems (I cite the scene where he panics when he's told the Mark 42 isn't charging, forcing him to calm down when the kid suggests he builds something. This results in him creating a series of homemade weapons to continue in his task until the suit was ready. Tony using those weapons was the first step in him no longer needing the suit. And, of course, the Clean Slate protocol scene seemed like Tony purging himself of all the suits because he no longer needs them as a crutch. The removal of the Arc Reactor and the shrapnel that it was keeping from going to his heart also backs this up even more). To me, Iron Man 3 was the closing of the Tony Stark/Iron Man phase. Now, Tony can move on to appearing as being himself without the suit.
