Emulator

Sounds like you're using WJoy on OS X to connect the thing. I seem to have been the first to run into this issue, and instead of changing the radius (the build of Dolphin I was using came before that option was put in), which might not work perfectly depending on the controller's calibration (for me, the sticks aren't equal in all directions this way), the fix I found was to add two of the axes together for each stick direction:

Main Stick/Up = Axis Y-+Axis Y+-
Main Stick/Down = Axis Y++Axis Y-+
Main Stick/Left = Axis X-+Axis X+-
Main Stick/Right = Axis X++Axis X-+

C-Stick/Up = Axis Rx-+Axis Rx+-
C-Stick/Down = Axis Rx++Axis Rx-+
C-Stick/Left = Axis Z-+Axis Z+-
C-Stick/Right = Axis Z++Axis Z-+

Either paste those into a controller profile .ini or right-click each stick direction and paste the corresponding line into the box.

I don't know why the actual fuck this is required (the WJoy dev shrugged and said he's using the same exact stuff for the normal Classic Controller, which doesn't have this issue), but I'm pretty sure this isn't really a Dolphin-specific issue regardless.

Actually I'm using Linux... and even thought the sticks aren't equal for me as well I think that there are controller out there that could need the additional radius to have a work around.I wouldn't be comfortable to tell people to edit the ini file to get it working.
Maybe there should be a auto config routine. (Turn the sticks around and use the reading to set it as maximum so controller are configured perfectly)

Huh, wow, so it's a controller-specific thing, not WJoy's fault. Interesting.

Calibration and extra radius are pretty decent workarounds, but I think the not-equal-in-all-directions issue makes this kind of a unique case. I'd personally just include default profiles for various controllers with Dolphin, but that'd require some work to implement nicely. v_v

Not being equal is no problem for me,since the discrepance is minimal.I got problems when configuring it though cause I either had to press the left stick harder to the side to be recognized or (what I did) enter the right button description manually.It's not that this issue makes any game less playable.

You could also add wiimote like dolphin support for the wii u pro gamepad :)

Then we may as well also support using a Classic Controller for GC games. This and default controller profiles are features I'd love to see in Dolphin.

Oh btw with your settings from post 2 it works without my modications.I only had to switch up and down for linux

Is there anyway you can build dolphin for mac with this patch and post it? I have the same problem as you, and I have tried building it myself but I'm a windows guy and I'm not too fluent on building and compiling things in linux/unix. (I just got a macbook pro with retina display & discrete graphics so i would really love to have this running on there.)

Pauls fix worked.Just edit the config

I did Paul's fix exactly, but my controller's input still doesn't register correctly. My left analog stick won't register left or up, and my right analog stick wont register left. Although when I press in the analog sticks and push in a direction it registers it correctly. Sort of like pressing R3 and L3 on PS2 controllers, but then doing that while pushing a specific direction.

Also I just managed to finally get it to build, if you could tell me the process/syntax for applying patches to a build I would still like to try using your patch.

git apply /path/to/patch.patch

Also, if the stick's not working right, you probably didn't configure it right. Works perfectly fine for me...

Thanks Paul. I'm using the Wii U Pro controller, not the gamepad if that makes any difference. And you were actually right. I don't know why, but for the main control stick I need to follow your config and also add 'Button 24' for each setting. And I also need to add a 'Button 25' for the Z axis settings on the C-stick. So my config looks like this:

Main Stick/Up = Axis Y-+Axis Y+-+Button 24
Main Stick/Down = Axis Y++Axis Y-++Button 24
Main Stick/Left = Axis X-+Axis X+-+Button 24
Main Stick/Right = Axis X++Axis X-++Button 24

C-Stick/Up = Axis Rx-+Axis Rx+-
C-Stick/Down = Axis Rx++Axis Rx-+
C-Stick/Left = Axis Z-+Button 25
C-Stick/Right = Axis Z++Button 25

But now it actually works.