When questioned about the structure of Index's development going forward, Tsurumi stated that Sega has "no plans to undertake any of their work" and that Index will be "working as an independent company."
With that said, Tsurumi said he would "love to have them utilize any of Sega's dormant IPs." It's kind of fun to think what Atlus would cook up with the Jet Set Radio or Space Channel 5 franchise, especially with their upcoming venture onto the dance floor. Of course, a new Valkyria Chronicles might make a lot more sense, given the studio's reputation with RPGs.
Update: This article originally credited the involved interview to Siliconera. While Siliconera provided a translation, the interview was conducted by Famitsu magazine. We apologize for the mistake.