SOLVED
Hi again, yes it's my old post, but it took me so long to find out this simple solution, I just couldn't see it, grrrr. So, when you create configurabe item, well actually his product configurations, you can click and pull the entire box containing the attribute values up or down mith the mous, and define the sort order of them. So if you want to have attribute Size appearing before Color, you just pull it higher.
Meanwhile, I've tried also customizing the code, I've found info somewhere on Google and it involved changing the code in file vendor/magento/module-configurable-product/Model/ResourceModel/Product/Type/Configurable.php, the modification is marked with "custom_file_entry" tags. This worked for me, but is not a proper solution, because you'll lose this on magento update. So the way to go, would be to create a module for this. But to be honest, an entire module just for this sorting fix...no I'll stick the mouse pulling for now 
public function getAttributeOptions($superAttribute, $productId)
{
$scope = $this->getScopeResolver()->getScope();
$select = $this->getConnection()->select()->from(
['super_attribute' => $this->getTable('catalog_product_super_attribute')],
[
'sku' => 'entity.sku',
'product_id' => 'super_attribute.product_id',
'attribute_code' => 'attribute.attribute_code',
'value_index' => 'entity_value.value',
'option_title' => $this->getConnection()->getIfNullSql(
'option_value.value',
'default_option_value.value'
),
'default_title' => 'default_option_value.value',
]
)->joinInner(
['product_link' => $this->getTable('catalog_product_super_link')],
'product_link.parent_id = super_attribute.product_id',
[]
)->joinInner(
['attribute' => $this->getTable('eav_attribute')],
'attribute.attribute_id = super_attribute.attribute_id',
[]
)->joinInner(
['entity' => $this->getTable('catalog_product_entity')],
'entity.entity_id = product_link.product_id',
[]
)->joinInner(
['entity_value' => $superAttribute->getBackendTable()],
implode(
' AND ',
[
'entity_value.attribute_id = super_attribute.attribute_id',
'entity_value.store_id = 0',
'entity_value.entity_id = product_link.product_id',
]
),
[]
)->joinLeft(
['option_value' => $this->getTable('eav_attribute_option_value')],
implode(
' AND ',
[
'option_value.option_id = entity_value.value',
'option_value.store_id = ' . $scope->getId()
]
),
[]
)->joinLeft(
['default_option_value' => $this->getTable('eav_attribute_option_value')],
implode(
' AND ',
[
'default_option_value.option_id = entity_value.value',
'default_option_value.store_id = ' . \Magento\Store\Model\Store::DEFAULT_STORE_ID
]
),
[]
)->where(
'super_attribute.product_id = ?',
$productId
)->where(
'attribute.attribute_id = ?',
$superAttribute->getAttributeId()
//>custom_file_entry
// solution taken from: http://magento.stackexchange.com/questions/141899/configurable-product-attribute-sort-order-in-dropdown-2-12
//);
)->joinInner(
['attribute_opt' => $this->getTable('eav_attribute_option')],
'attribute_opt.option_id = entity_value.value',
[]
)->order(
'attribute_opt.sort_order ASC'
);
//<custom_file_entry
return $this->getConnection()->fetchAll($select);
}
/**
* @return ScopeResolverInterface
* @deprecated
*/
private function getScopeResolver()
{
if (!($this->scopeResolver instanceof ScopeResolverInterface)) {
$this->scopeResolver = ObjectManager::getInstance()->get(ScopeResolverInterface::class);
}
return $this->scopeResolver;
}