The games which make the best use of the dual screens and touch screen are designed specifically for the DS--Canvas Curse, EBA, Meteos and so on. CT...wasn't designed for the DS. I'd be happiest to see something C:PoR-esque--a map/menu toggle on the second screen would be lovely. I loves me some maps.
Touch screen controls could be okay, so long as they aren't the only form of control and they can be turned off. The Pokemon Mystery Dungeon games are the only games I know of that allow you to turn off touch screen capabilities--very nice. It even lets me keep the controls on for menu navigation (and off for everything else) if I want, which is handy, cuz menus in the roguelikelike's a real...pain.