According to a article from Hindustan Times Irrfan Khan is supposed to return as a villain in the Amazing Spider-Man 3 here's a quote from that article.
"Irrfan and Marc (Webb; director) share a great rapport ever since he worked in the first part. And although his role was a small one, Marc has been keen to work with Irrfan again. Things are yet to be finalized,” says an insider."
But here's the problem with him returning(Spoilers from TASM) HE'S DEAD!
In a deleted scene from The Amazing Spider-Man( Which you can watch below) Dr. Ratha is killed by the lizard in his attempt to stop him from turning the people of New York into Lizard people also a article from the Daily Bugle tumblr page it states that he's been missing days before \
The Amazing Spider-Man 3 is set to release in 2016.