There's always a performance/complexity/fidelity tradeoff with Magento, and the only way to overcome it is to pull up your sleeves, suffer through a few bad imports, and learn what works best for your situations.
Two things that may be of interest to you. First, make sure your WSDL cache is on. Many of the V2 SOAP API performance problems can be traced back to PHP not caching the WSDL file.
Second, considering writing native PHP scripts that use the native PHP API objects. I don't mean models like Mage_Catlog_Model_Product
, but API objects like
$model = Mage::getModel('customer/customer_api');
var_dump(get_class($model);
These objects are where the business logic for RPC/SOAP API code lives, and if you can call them directly you avoid a lot of the performance problems related to the WS API overhead.