I tried this model with FastCommander, with my own website, own shop webservice backed FastSpring payments. Maintaining these all is a PAIN IN THE ASS. Never again.

Published my new app (SynoTool) to the App Store. From the very beginning there are more installs, maintaining this all is easier, faster (at least for me), and I can sleep without worrying if there are any bugs in my licensing code on client or backend side.

Besides, as a user, I love apps distributed with App Store. I have more trust in Apple, than to developer who does not want to pass Apple security, compatibility validation and usability review.