I think I'll throw out the the SMT: Devil Survivor games on DS. Buy the overclock version of the first one if you have a 3ds. They are great rpgs with turn based with real time tactics combat and branching story lines with a lot of endings.
Another underrated game is 999: nine hours, nine doors, and nine persons for DS.Its a mystery novel type game with puzzle elements worked in. Also check out its sequel Zero Escape:Virtue's Last Reward on 3ds and Vita.