Well, I played The World Ends With You as well. On the DS (since we've been talking about iOS games, I was unsure if it had an iOS port. I can't see how it could work, what with losing the dual screen features, losing the stylus, and having your hands cover ninety percent of the action, but Square has done crazier things). Designed for touch controls. Honestly, I wasn't too impressed. You control the upper screen character completely with the buttons, and I didn't see why the same controls couldn't have worked for the character you control. You could have streamlined out one screen to DPad, one to buttons, and it would have worked great. Yeah, you'd lose the ability to move your character, but there is almost no tactical depth there anyway. The World Ends With You was probably the best touch-control-only games I've played, but it still didn't do enough to justify it as a control scheme, because it didn't do anything that I could do with buttons (and, honestly, couldn't do easier, as the repeated swiping did get repetitive and tiring far more quickly than button presses).
Also, YOU were the one who brought up Chrono Trigger in defense of touch controls. If Chrono Trigger is one of the better jobs they've done implementing touch controls, I think my point is proven. If not, maybe you shouldn't have brought it up and should have instead listed some games that actually use the features well.
If there are good games that use touch controls, I'm willing to try them. But I've played a lot, and a lot of games designed for touch controls by other companies, and I have never seen value to them as a primary control scheme.
Sword of Mana was alright, but I agree. Even fewer good games that have actually been released over here. I'll just try to enjoy Secret of Mana and pray it gets rereleased for the 3DS (alongside other SNES titles like Illusion of Gaia, Super Mario RPG, and Super Metroid).