Did you update optimiser statistics for all tables on which you created indexes after you created them? If you did not then there is a high possibility that the new indexes will not be used. Also, how did you determine what new indexes are needed? ANd finally, what TimesTen release are you using?
For Exalytics, if supported and certified by the other components right now we would recommend using TimesTen 126.96.36.199.1. In addition, the best way to determine the optimal indexes for BI queries is to use the TimesTen Index Advisor. Please consult the details of the builtin procedures ttIndexAdviceCaptureStart, ttIndexAdviceCaptureEnd, ttIndexAdviceCaptureOutput and so on in the TimesTen Database Reference.