From a post on the Iron Man Message Board, in response to the removal of Tony Stark's innate bio-abilities
If Iron Man retained the Extremis nanotech capabilities, but kept fighting super-villains, he'd trounce them easily. Not only would the already troubled dramatic tension of franchise superhero comics be further reduced, but Tony would almost come across as a bully for only fighting weaker enemies. Fiction favors the underdog-- another reason Tony is hard to write, because he's a rich genius who built his empire on military-industrial blood money.
This is why once Tony became Extremis enhanced, he stopped fighting villains ( except for cases like the Inevitable, which was meant to prove that he couldn't be bothered with costumed thugs anymore ) and went to bigger challenges; instead of just saving the world, he was trying to fix it. The Project ARGONAUT team of remote-controlled Iron Men was a precursor to this mentality, but the Director of SHIELD role was even more ambitious-- he'd gone from making Iron Man security for Stark International to security for the world. Which made the threats he faced even greater-- Ezekiel Stane being the harbinger of the new era, someone who spread super-terror on a level that not even Tony's awareness could match.
Of course, Tony DID match Zeke, but only by destroying his company and killing several of Zeke's cohorts. Which really unsettled Tony-- that story ended with him realizing that in order to fight that kind of brutality, he'd have to become more brutal himself. It's not about him being a human who uses the best of his species' abilities to compete with gods and monsters, but about a human who excises his species' innate capacity for good to compete. Note how this is the way many of Marvel's great villains started; Doom, Magneto, the Ghost, and others had good intentions, but they perverted themselves to the point where they couldn't even act decent any longer.
The problem with power is that even if you try to amass it for good reasons, somebody else is going to amass more of it in response, and then it becomes a vicious cycle. With Tony, this is mixed in with his self-loathing ablism-- wether he admits it or not, he wants the progressively increased strength of the Iron Man to compensate for his own failings. It's no coincidence that his greatest invention is a human prosthesis, that enhances his capabilities but hides his humanity. With the Iron Man, and especially with the Extremis enhancile that eradicated the barrier between man and armor, Tony used technological power to eliminate weakness, as opposed to accepting it. And hence, greater power leads to greater opposition.
Now, Tony Stark's failures have given us Norman Osborn's empire-- a man who has basically become a homunculus of Tony's sins. The system of SHIELD directors went from Nick Fury, who had to make hard decisions but whose sympathies ultimately lay with his constituents ( especially his troops ), to Tony, who made even more controversial decisions in the name of an ambiguous " better tomorrow ", to Norman, who does horrible things simply to serve his own ego. The Marvel power struggle in which Tony was so instrumental created an environment where a madman could become America's greatest hero through clever PR. Which left Tony a disgraced fugitive, feeling responsible.
This makes Tony's self-destruction in the current storyline an attempt to find a different solution, since gaining power had failed him and endangered others. Tony's new plan inverted his previous methods in an almost religious fashion-- stripping himself of all abilities until he's completely helpless. Not only because he didn't want his nanotech-enhanced brain falling into Norman's clutches, but because he wanted to break the cycle. On an ideological level, it worked very well-- his televised conflict with Norman had him severely handicapped, unable to speak in complete sentences, unable to operate any Iron Man except for the crude Afghanistan prototype, and barely aware of what was going on. By contrast, Norman appeared to the world as the complete monster the heroes and the audience know him to be, and without the Green Goblin persona to deflect his cruelty. When Norman beat the impaired Tony half to death, his power lost much of its meaning-- viscerally, there's no way for him to spin that kind of sheer cruelty.
I expect that once Tony's mind is put back together, he'll go back to being a man in a suit, without all the nanotech enhancements. He won't be as powerful as he used to be, though he won't be intellectually impaired either. But as a symbol, he'll be closer to what he wanted to be-- a man who uses his machines to oppose those who would kill and oppress others, instead of a man who uses machines to make more powerful machines for intangible benefits.