The touch screen controls didn't annoy me much, but the fucking mic bits on those games did. Having to shout into the mic to pass certain bits on Phantom Hourglass were the worst part of the game, especially if your playing in public, but fortunately you could bypass them by blowing into the mic. Talking of blowing into the mic, the flute in Spirit Tracks... I loved the idea, and it sounded awesome and I liked it. Except my mic on my DS didn't work well, so it took me about 10 minutes to trying to play some of the final songs because it just would stop registering my blows halfway through a tune. Fortunately I never had similar problems with the item that required you to blow into the mic.
The touch screen controls were actually utilised quite well I thought, far better then most games on the DS. Few ever seemed to actually use them significantly, but Phantom Hourglass had some nice ideas. The only irritating parts where when a puzzle or optional goodie required note taking or precision drawing. Mostly because I'm a messy writer at the best of times, and drawing a straight line or writing a concise note on the DS touch screen was awkward at the best of times. Apart from those few cases, they were used brilliantly I thought. Stylus control of the boomering was far less annoying then I had originally expected, and same with some of the drawing puzzles (which fortunately realised that precision was awkward and were incredibly forgiving of vaguely wonky lines or imprecise stylus handling). The combat was suprisingly good and the games actually had an ability to be genuinely challenging at times. The final stage of the final boss in Phantom Hourglass could easily take the cake of the hardest boss in any Zelda game ever, if he took one or two more hearts off per strike. Even so, I beat him with fairly low health and both potions used up. Shame you could cheat your way past the final fight if you abused the mechanics, because there were some really, really awesome ideas there.