The "real" Mandarin would have lead into taking on those issues you mention.
Killian did start to address it - Extremis did bring up posthumanism with its regenerative qualities, but it was too little, too late.
I think the real appeal of Tony Stark lies in the irony that as he becomes less physically human, he becomes more relatable to the audience as a person. He goes from being a billionaire playboy who is callous and unsympathetic to the suffering he inflicts on the world, to being dependent on technology to survive and inspired to make something more of himself. It's an interesting paradox because at the same time he needs to balance out his dependence on technology lest he lose touch with his humanity altogether. And unlike other heroes, he is very, very vulnerable to these flaws, and there are serious consequences to his actions;
Age of Ultron is a realisation of this lapse.
But when it comes to
Iron Man 2 and
Iron Man 3, I think Marvel just saw the audience responding to an action hero with a happy-go-lucky streak at a time when the genre was taking itself far too seriously, and just moved to recreate that.
Ultron was also "killed off".
He kind of had to be. I know that he's a recurring villain, but if he was only thwarted and came back later, I think the over-arching story would lose momentum because it would feel like there was no tangible progress. Especially since the Avengers only prevented the invasion in
The Avengers rather than completely destroying the threat; if they stopped Ultron without destroying him, they would be zero for two.
I was disappointed with how they handled IM2.
I think a lot of people were. The film did have a couple of interesting ideas, like the stress and unitended consequences of being a superhero, but I think the problem was that Jon Favreau only really tried to replicate the original film's success. Mickey Rourke was wasted, and Justin Hammer was a cheesy version of Obadiah Stane (but full credit to Sam Rockwell for running with it without resorting to hamming it up).
But mostly, I can't take the film seriously because it would have us believe that the quickest way from Casino Square to Tabac is to go backwards around the circuit.