Wasn't it Team Plasma behind Genesect's alterations? I'm not sure if they plan to use Team Plasma again, although they did reuse Team Rocket from GSC. It would make sense if Team Plasma gets reused, since their theme concentrates on the Tao trio (Zekrom, Reshiram and Kyurem) after all.
If however they go with the new evil team approach, then we only have a few leads for that. From the looks of it, they will probably base it on Kyurem's Ice-typing, or at least on whatever Kyurem's theme is. Sounds too typical, now that I think of it, and I think Game Freak will be more creative than that.