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.