How do I change character direction without messing up the controls?

Okay, it got resolved now. Here's the final Code, for other people struggling with this:

 if (controller.isGrounded) {
         transform.forward = Vector3.Normalize(new Vector3(Input.GetAxis("Horizontal"),0,Input.GetAxis("Vertical")));
         moveDirection = transform.forward;
         if (Input.GetAxis("Vertical") == 0 && Input.GetAxis("Horizontal") == 0) {
             moveDirection *= 0;
         }
         else {
             moveDirection *= speed;
         }
         
         if (Winp.GetButtonDown(WiiUGamePadButton.ButtonA) || Input.GetKeyDown(KeyCode.Space)) {
             moveDirection.y = jumpSpeed;
         }
         Debug.Log(moveDirection);
     }

I can see why you are having problems, but it is hard to know the best way to fix it. The way your code is written now, 'Vertical' trumps. That is, if you are using a joystick, then giving it a lot of horizontal and just a bit of vertical will still result in looking in the 'Vertical' direction (which means it should move in the 'Vertical' direction). Here is a guess at what you want. You may still need to figure out if your rotation code works like you want in all situations:

 if (controller.isGrounded) {
     var moveMag = new Vector3(Input.GetAxis("Horizontal"),0,Input.GetAxis("Vertical")).magnitude;
     moveMag *= speed;

     if (Input.GetAxis("Horizontal") < 0) {
        transform.eulerAngles = new Vector3(0,-90,0);
     }
     if (Input.GetAxis("Horizontal") > 0) {
        transform.eulerAngles = new Vector3(0,90,0);
     }
     if (Input.GetAxis("Vertical") < 0) {
        transform.eulerAngles = new Vector3(0,180,0);
     }
     if (Input.GetAxis("Vertical") > 0) {
        transform.eulerAngles = new Vector3(0,0,0);
     }

     moveDirection = transform.forward * moveMag;

     if (Winp.GetButtonDown(WiiUGamePadButton.ButtonA) || Input.GetKeyDown(KeyCode.Space)) {
        moveDirection.y = jumpSpeed;
     }
 }

You mentioned you don't want to do a lot of changes, so you might end up not implementing my suggestion. But the best way, in my opinion, is to divide the possible analog stick movement space into four areas, each 45 degrees wide.

Imagine a big circle, let's say it has a radius of one. Now imagine an X at the center which touches the circle at four points. Let's call the newly created uppermost sector 'up', the one on the left, 'left' etc.

What you need to do is determine which sector the analog stick is currently in. Because Unity gives the analog input between 0 and 1 in both vertical and horizontal, our analog stick input can be considered a vector within our circle. This is exactly what you're doing in line 2.

Instead of then comparing the length of the individual axes, you should be using a reference forward direction - in third person games it's usually the camera's forward - and computing the angle of the analog stick vector and our reference forward. Our reference direction is at angle 0 and pointing straight up.

• If the angle is between 0 and +/- 45, look forward

• if between +/- 45 and +/- 135 than look left or right, depending on sign

• if between +/- 135 and +/- 180 look backwards.

Moving should of course be done in the direction and speed of the analog stick vector.

I can't remember if it's possible to get a (+/-1,+/-1) out of Unity's input system. if it is, then instead of a circle, use a box.

EDIT: for some reason I had divided everything by two in my math. Fixed now.

EDIT: I cobbled together what I meant in code:

             Vector2 inputVector = new Vector3(Input.GetAxis("Horizontal"),Input.GetAxis("Vertical"));
             
             moveDirection = transform.TransformDirection(new Vector3(inputVector.x,0f,inputVector.y));
             
             float angle = Mathf.Atan2(inputVector.x,inputVector.y)*Mathf.Rad2Deg;
             
             if(angle>=0){//the right side
                 if(angle<45f){
                     //rotate character facing forward
                 }
                 if(angle<135f){
                     //rotate character facing right
                 }if(angle<=180f){
                     //rotate character facing right
                 }
             }else{
                 if(angle>-45f){
                     //rotate character facing forward
                 }
                 if(angle>-135f){
                     //rotate character facing right
                 }if(angle>=-180f){
                     //rotate character facing right
                 }            
             }