Well , it was nearly impossible to control the tornado launcher with the motion control and I kept losing in the decryptor mini games until they asked me to use the joystick
They all work fine to me, except for the the laser beam and the tornado launcher…
I never had any problem at all with the SIXAXIS in ToD.
I loved the sixaxis control in TOD because it created a new dimension which the previous games of Ratchet and Clank didn't have.
The SIXAXIS controls in Tools of Destruction are what makes the game very new different and FUN! At first i didn't think so. When i played it for the first time and was flying in the air i was unsure of what to do? I hadn't a clue? Then i noticed the controler was making him move! So as i began to move Ratchet away from cars and ships it was done. Then at Stratus City i got another go at it! It was soo fun! And then later on i brought the Tornado Launcer. Hadn't a clue what it did? Just a Tornado that either sits there or makes it way around randomly? How strange? I was thinking why couldn't it be more guided and get enimies? But moving on to the first Robo Wings i recognised the keywork SixAxis! So i moved my controller around and much like the glider i went up, down, left and right. Was fun and hard but i eventually got the hang of it. The trick is not to move your controller any more than about 90 degrees either way. Start flipping your controller and it gets hard. I find many many people are making the same mistakes, and that makes it hard for them. I was amased about how smooth it all worked! It all went along so well! Then i remembered the word Sixaxis had something to do with the Tornado Launcher? So i then found that moving the controller moved the tornado! But it was too hard at the time so i avoided useing it.
Later on the Geo Laser came in and i thought WOW this is harder! The controles were not smooth! They were all… Wierd and hard to use? Then i eventually grew to hate that part… The Decrypter was the same story but i did think it was really creative! And hard to master? But at the return the the fight festival i found the secret decrypter and once i did that all the rest were a piece of cake! Exept on Igliak it got a bit hard. The Holo Pirate Disguise was not very creative at all! I hated that for the reason that it was so… Easy! After a few Decypterfails in challenge mode i found you could switch to the analouge stick… I loved it at first but it made everything… Not as fun IMO eventually for a change i switched back and decided to attemt to master the Sixaxis. It took me a while but i mastered the Robowings and they became easer than… Well? I dunno? They just got easy. Then the Decyptor was a challenge! It was hard but i got through about two challenge modes with the occasional fail… Then found out you could hold the ball in one place with x!!! This changed alot! And eventually i learnt that the controls werent stuffed. It was me! I just sucked! Then i tried to get good at the Tornado Launcer! It took FOREVER! But i got good enoth at it to control; the Tornado AND other tasks! (like fighting with another gun) Oh and before i mastered the Tornado i got good at the Geo Laser! Why did i do all this? Because at the time i decided to get good at these i was playing other games and had noticed something very important… They either had no Sixaxis, or the Sixaxis sucked. Much like the Dynamo. Uh that was a massive let down 
In my opinion, I disliked using it 
I only used it to control the weapons and devices that used it XD