In the beginning of Iron Man 3 when Extremists attack on his house, he uses his suit to save Pepper's life. The same could be done in the end part of the movie when Pepper Potts was falling from 200 feet. Why didn't he do it?
The suits were under the command to engage and eliminate all Extremists. The suits considered Pepper too as an Extremist as she had been injected with the virus. Therefore, the suits would try to destroy her rather than save her.
And, IMO issuing a new command to save Pepper Potts would had taken time and moreover be seen as an ambiguous instruction by the suit's system.
The MK42 was a prototype, thus it was the only one that he had that he could send onto her body or summon to his own. The only one that had those gesture controls from when he injected himself with transmitters in the beginning of the movie. After pepper falls is when he is up top with Aldrich and he says "The prodigal son returns." meaning MK42 was in bound. MK42 then crashed and fell into pieces and he never put it on again. But he wasn't able to order any other suits to attach to her in that period of time. The only way he ever got caught in a suit was from timing his jumps and Jarvis having his back. But there were a lot more suits at that point.
The Extremis was created as a way of recovering and rebuilding a body. It could activate when a body got injured. Maybe that's why Jarvis' systems started considering Pepper as an Extremist and didn't try to save her when she was falling and attempted to kill her when the virus activated. As for me, though, I was expecting the suit to catch Pepper till the end)))