Full integration with Prestashop rather than just via database. Prestashop (and others) have scripts and functions that are initiated when activities in the back office are undertaken (such as marked order shipped) which is not supported by the current level of integration.

If the original poster can see this: I found this googling to make a final check if somebody had already done my work for me.. Since they have not, I am writing a module for this right now since I have same issues with wanting prestashop's hooks to run when updating order status rather then just inject the status into database. You can email mnowak@purecigs.com if you'd like a copy when done hopefully within next 24 hours.