If you use the Commerce Fancy Attribute module you'll see that your product variations are in a different order than the product attribtues. The solution I'm going to show here is a simple custom code to solve that issue.

The solution is specific to the project and you may be find it useful to create a generic solution too.

/**
 * Implements hook_element_info_alter().
 *
 * Alter the fancy attributes element.
 */
function MODULE_NAME_element_info_alter(&$type) {
  $type['commerce_fancy_attributes']['#process'] = array('MODULE_NAME_fancy_attributes_process_radios');
}

In the element process function we first load the node:

    $nid = $form_state['build_info']['args'][2]['entity_id'];
    $node = node_load($nid);

Then you look up the attributes and product variation delta relationship:

    $node_wrapper = entity_metadata_wrapper('node', $node);
    $products = $node_wrapper->field_product->value();
    $attributes = array();
    foreach($products as $delta => $product){
      if(isset($product->ATTRIBUTE_FIELD) && !empty($product->ATTRIBUTE_FIELD)){
        $attributes[$product->ATTRIBUTE_FIELD[LANGUAGE_NONE][0]['target_id']] = $delta;
        }
      }

Then you change the fancy attribute weight values for the radio button:

$weight = $attributes[$key];

The complete process function:

/**
 * Process function for the commerce_fancy_attributes element.
 *
 * Each radio button gets a description containing the rendered term.
 * This description is hidden by default. Then, if JS is enabled,
 * the radio button and label are hidden, the rendered term in the
 * description is shown and made clickable.
 */
function MODULE_NAME_fancy_attributes_process_radios($element, &$form_state, $complete_form = NULL) {
  if (isset($element['#options']) && count($element['#options']) > 0) {
    $tids = array_keys($element['#options']);
    $terms = entity_load('taxonomy_term', $tids);
    $render_terms = entity_view('taxonomy_term', $terms, 'add_to_cart_form');
    $render_terms = $render_terms['taxonomy_term'];
    $nid = $form_state['build_info']['args'][2]['entity_id'];
    $node = node_load($nid);
    $node_wrapper = entity_metadata_wrapper('node', $node);
    $products = $node_wrapper->field_product->value();
    $attributes = array();
    foreach($products as $delta => $product){
      if(isset($product->ATTRIBUTE_FIELD) && !empty($product->ATTRIBUTE_FIELD)){
        $attributes[$product->ATTRIBUTE_FIELD[LANGUAGE_NONE][0]['target_id']] = $delta;
        }
      }
    $weight = 0;
    foreach ($element['#options'] as $key => $choice) {
      // Maintain order of options as defined in #options, in case the element
      // defines custom option sub-elements, but does not define all option
      // sub-elements.
      // $weight += 0.001;
      $weight = $attributes[$key];
      $element += array($key => array());
      // Generate the parents as the autogenerator does, so we will have a
      // unique id for each radio button.
      $parents_for_id = array_merge($element['#parents'], array($key));
      // Render only the visible children of the render array, to prevent
      // unneeded markup.
      $render = array();
      foreach (element_get_visible_children($render_terms[$key]) as $child) {
        $render[$child] = $render_terms[$key][$child];
      }
      $output = drupal_render($render);

      $default_value = isset($element['#default_value']) ? $element['#default_value'] : NULL;
      // Wrap the description with a div specifying the term ID.
      $class = array('term-' . $key);
      if ($key == $default_value) {
        // Add a class specifying this is the currently selected radio.
        $class[] = 'description-selected';
      }
      $output = '
' . $output . '
';

      $element[$key] += array(
        '#type' => 'radio',
        '#title' => $choice,
        // The key is sanitized in drupal_attributes() during output from the
        // theme function.
        '#return_value' => $key,
        '#default_value' => $default_value,
        '#attributes' => $element['#attributes'],
        '#parents' => $element['#parents'],
        '#id' => drupal_html_id('edit-' . implode('-', $parents_for_id)),
        '#ajax' => isset($element['#ajax']) ? $element['#ajax'] : NULL,
        '#weight' => $weight,
        '#description' => $output,
      );
    }
  }
  return $element;
}