I agree that the autopatching makes the patches harder to read. My autopatching is really only done to get around limitations of interfacing with Pd to get certain objects called up the way that I want them to be. I'm actually starting to replace all that with Thomas Grill's [dyn~] which is making everything so much easier and should make things more legible once the display for [dyn~] gets more functional.
actually the possibility to display a dyn~ patcher is really inofficial (and practically useless) at the moment... maybe there will be a different way of debugging dynamically created objects and connections.
best greetings, Thomas