PlayerController.cs

public class PlayerController : MonoBehaviour {
    [SerializeField] private Rigidbody _rb;
    [SerializeField] private float _speed = 5;
    [SerializeField] private float _turnSpeed = 360;
    private Vector3 _input;

    private void Update() {
        GatherInput();
        Look();
    }

    private void FixedUpdate() {
        Move();
    }

    private void GatherInput() {
        _input = new Vector3(Input.GetAxisRaw("Horizontal"), 0, Input.GetAxisRaw("Vertical"));
    }

    private void Look() {
        if (_input == Vector3.zero) return;

        var rot = Quaternion.LookRotation(_input.ToIso(), Vector3.up);
        transform.rotation = Quaternion.RotateTowards(transform.rotation, rot, _turnSpeed * Time.deltaTime);
    }

    private void Move() {
        _rb.MovePosition(transform.position + transform.forward * _input.normalized.magnitude * _speed * Time.deltaTime);
    }
}

public static class Helpers 
{
    private static Matrix4x4 _isoMatrix = Matrix4x4.Rotate(Quaternion.Euler(0, 45, 0));
    public static Vector3 ToIso(this Vector3 input) => _isoMatrix.MultiplyPoint3x4(input);
}

I was researching about this problem, cause i`m having it too. I think all the problem is related to the use of RigidBody to movement calculations. They recomend use another method to calc the movement...
Did you find something new about this problem?

I fixed this by freezing the rotation axes on the Rigidbody and the Y position

I was researching about this problem, cause i`m having it too. I think all the problem is related to the use of RigidBody to movement calculations. They recomend use another method to calc the movement...
Did you find something new about this problem?

I fixed this by freezing the rotation axes on the Rigidbody and the Y position

Thank you very much for the reply!
I'l gonna try this on my project, but in any case, using the rb.MovePosition makes the object ignore other objects with coliders... all this factors limits the possibilities on the project, like Jumping or running fast or dashing.

with this code, it's impossible to control the magnitude of the movement with a joystick, is it possible to fix this?

with this code, it's impossible to control the magnitude of the movement with a joystick, is it possible to fix this?

You can normalize the vector, so if its 0, the magnitude is 0, otherwise is 1. Done that, you can simply play with the speed variable to have an "on/off" movement or add some acceleration time based.