I would have to say chain of memories for the gba because I didn't like how the controls where laid out in the game.

Kid Icarus: Uprising. The controls were a bit weird to get used to at first when you play it. But after a while you kinda get used to it.

KH1. I played KH2 first so the difference in the camera moving irritated me.

I had so much trouble with Katamari Damacy's controls that I could never get passed the first level.

Brothers: A Tale of Two Sons (on the PS3). First one that comes to mind as being weird and disorienting as firetruck.

Super Mario Bros. 2 for the 3DS. Idk, it just feels weird D: especially when sprinting. But yeah, I'm going to have to agree with Tails as well. Kid Icarus: Uprising really had some wacky controls. Using the touchscreen to aim is annoying at first, but I got used to it after a while. It's annoying when using it in multiplayer though. I have to zigzag the stylus to aim at multiple people like a crazy dude. 

The World Ends with You. Never beat that freaking game because of how strange the battle system was. 

the zelda CDI games and a lot of the games from action 52

The World Ends with You. Never beat that freaking game because of how strange the battle system was. 

i freaking loved the battle system! TWEWY is one of my favorite games of all time!

Kid Icarus: Uprising. The controls were a bit weird to get used to at first when you play it. But after a while you kinda get used to it.

i actually adapted right from the start. i guess its becouse ive been waiting ever scince the game was announced and visualized/tried it in my head.

For me... It only has to be a section of a game, and that was Assassins Creed 2 during the flying machine missions. 

There are some nes games that have controls that I have to say doesn't use common sense like these games in the video below. 

Silent Hill: Shattered Memories for the Wii. 

you use the Wii remote for the flashlight, running, combat....

But the nunchuck is for looking, talking, and walking. 

Craziness. 

Does QWOP count?

Does QWOP count?

As long as it's a game that has bad controls to you. 

Dissidia 012: Duodecim. Hands down. Weirdest stinking controls ever....and most confusing.

ANYTHING WHERE YOU USE 2 JOYSTICKS AT THE SAME TIME TO CONTROL 2 CHARACTERS (Ibb/Obb, Brothers)

Any game that doesn't have a left handed feature when it needs one (Pokemon X/Y Super Training, Kid Icarus Uprising, etc.). Lefties play games too ;_;

Katamari Damacy. Weird controls. Very weird. But get used to them and the game is amazing!

 

Same with Shadow of the Colossus.

 

And Luigi's Mansion.

Heavy Rain ¬_¬

Oh god I hate the game's controls they are awful. Thank you for showing this. 

Oh god I hate the game's controls they are awful. Thank you for showing this. 

This is the only game I couldn't make any progress because of the control.I'm usually able to get use to bad controls like in the old Castlevania games or Sonic Heroes,but that was too much awfulness for me to handle

The World Ends with You. Never beat that freaking game because of how strange the battle system was. 

 

I love TWEWY's battle system! But yeah, it kinda took awhile to get used to it... But once you do... it's the best thing ever.

For me the weirdest controls were in some Battlefield-game (cannot remember the number). I tried once and... uh, that was so akward. I realised then that FPSs aren't my thing.