I've just fiddled around a bit and my standard transcode settings for HB in the GUI are High Profile, then an RF of 18, the H.264 Preset slider set to veryslow, detelecine to Default, and then all English audio tracks and subtitles. It takes a long time to transcode, but it looks fairly good on a TV (via a Mac mini). My iPads (2 and Air) won't play these, but it looks like backing off the Preset one notch to slower will play. So for the iPad, anyway, it's the change between the slower and veryslow settings. I can see what the changes in the parameters are, but haven't delved into what the different settings really mean yet, and probably still won't know what is going on after that.
Between Mavericks and iOS7 it's sure been a downhill Fall for Apple software.