Number one for me is the ability to add in existing customers to the payment system. This has forced us to go to manual billing. It never occurred to me when I made the choice to move to DNP that this wouldn't be supported.
Outside of that - the general flow of the customer experience in relation to e-commerce could stand to be more intuitive. It's not instinctive for our new clients.
Despite my critical opening statement - I really do love DNP and see it as a significant improvement over Plesk/Helm for the Windows environment. My clients also love the look and feel of the user interface. The e-commerce portion is the weak spot and I'm very pleased to hear it getting some attention.