This control set up has worked so well for me I had to make a topic about it.  No more hand cramps. 
 
Set Aiming to the Circle Pad.  I had to tweak the speed a bit to feel like i could keep up and be as accurate as a stylus. 
 
Set Movement to the Face Buttons X, A, Y, B.  This works really well.  Double tap to doge and double tap and hold to sprint.  When pressing X to move forward, aiming with the circle pad controls the direction you go.  Navigation on foot is easy! 
 
It feels a lot like playing Starfox on the 3DS.  I imagine it feels very natural for leftys.  For me it took a level or two but then it begins to feel second nature.  I played around a bit with the controlls for attack on both the L button and R button.  I left it on the L button, it felt more natural. 
 
Try it out and give some feedback.  Would like to hear how other people have adapted to playing this sweet game.  Anyone using the stand? Or the circle pad attachment?

The game didn't need "fixing." I've been playing with the Circle Pad Pro and Stylus and have had no issues with comfort whatsoever.

@Hailinel: I have been playing with default controls and had no problems. But, keep in mind I also thought the similar controls in Metroid Prime: Hunters and Star Fox Command worked really well.

I think the default controls work well though I did change a lot of the sensitivities for the aiming and movement to get it down how I liked it. Tons of control options, I was really surprised.

@Hailinel said:

The game didn't need "fixing." I've been playing with the Circle Pad Pro and Stylus and have had no issues with comfort whatsoever.

I would consider the Circle Pad Pro as a fix. Nintendo really needs to admit the design fault of the 3DS and make a revision that has a second circle pad on the handheld.

@Andorski said:

@Hailinel said:

The game didn't need "fixing." I've been playing with the Circle Pad Pro and Stylus and have had no issues with comfort whatsoever.

I would consider the Circle Pad Pro as a fix. Nintendo really needs to admit the design fault of the 3DS and make a revision that has a second circle pad on the handheld.

I don't really call that a fix. The only thing that changes from that is that left-handed people are allowed controls that precisely mirror the standard controls. The game is otherwise perfectly playable without it. I consider broken controls to be controls that are unplayable under any circumstance.

@Scullinator said:

This control set up has worked so well for me I had to make a topic about it. No more hand cramps. Set Aiming to the Circle Pad. I had to tweak the speed a bit to feel like i could keep up and be as accurate as a stylus. Set Movement to the Face Buttons X, A, Y, B. This works really well. Double tap to doge and double tap and hold to sprint. When pressing X to move forward, aiming with the circle pad controls the direction you go. Navigation on foot is easy! It feels a lot like playing Starfox on the 3DS. I imagine it feels very natural for leftys. For me it took a level or two but then it begins to feel second nature. I played around a bit with the controlls for attack on both the L button and R button. I left it on the L button, it felt more natural. Try it out and give some feedback. Would like to hear how other people have adapted to playing this sweet game. Anyone using the stand? Or the circle pad attachment?

I've tried it, and I think it works well. My only concern is that the reticule movement is much slower, so while its useable on the standard difficulty, it might be an issue when you're betting hearts on the higher ones.

@Hailinel: If not "fixed", how about "improved in my opinion"?

@TruthTellah said:

@Hailinel: If not "fixed", how about "improved in my opinion"?

That's fair.

@Hailinel: Okay. Cool. I definitely think the default control scheme is serviceable, but I can understand why people might prefer Scullinator's solution. I'm glad he suggested it. :)

I thought I'd mention this on this off chance that no one has realised this by now. You CAN configure the circle pad pro to let you shoot using the big ZL button rather than the tiny, hard-to-reach, L button while still using the left circle pad to move. This might not help most people, but with my larger hands I find it very uncomfortable to hold the 3DS and use the circle pad + L trigger. Using the ZL trigger relieves a lot of the hand cramp. To achieve this, go to Control Configuration, select circle pad (left) for movement, then touch screen for aiming. Next, drag the Attack control over to the R trigger, which will mean that L will be bound to Align Camera instead. This will also mean that the ZL trigger on the Circle Pad Pro will now be used to shoot with when it wasn't before. It still won't magically make the game not crap to control, but for people will large hands like myself, it makes a big difference ergonimically.

Wow I'm surprised the game has remappable controls at all. Considering how much the controls are complained about one would have thought there was no way to change them.

But can you set aiming to face buttons and movement to slider? That has worked well on PSP.

@egg said:

Wow I'm surprised the game has remappable controls at all. Considering how much the controls are complained about one would have thought there was no way to change them.

But can you set aiming to face buttons and movement to slider? That has worked well on PSP.

Yes, you can.

@Hailinel said:

@egg said:

Wow I'm surprised the game has remappable controls at all. Considering how much the controls are complained about one would have thought there was no way to change them.

But can you set aiming to face buttons and movement to slider? That has worked well on PSP.

Yes, you can.

Remappable controls are great. =0

@egg said:

Wow I'm surprised the game has remappable controls at all. Considering how much the controls are complained about one would have thought there was no way to change them.

But can you set aiming to face buttons and movement to slider? That has worked well on PSP.

You can, but you'll lose pretty much all aiming fidelity by doing this. Can't help feeling that they dropped the ball big time by not letting you twin stick this game with the circle pad pro.

@Scullinator: the control works fine with me you need just to get used with it. I think it will help you a lot if you put "Autofire" On.