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For the 12.9 3rd generation wouldn't the 1080p 60 or 1080p 30 be better choices? Or is the extra quality not worth the speed and size difference? I have been using the Apple iPad Preset for a long time and just updated to HB 1.2.2 and notice it's gone. I don't normally tweak the settings myself, I've just been using the iPad preset which I know was 720, but I am wondering if I switch to 1080p30 or 60 will the difference be much better.
That being said, there shouldn't be much harm in using either preset, given an 720p source results should be equivalent. The 720p preset does boost the quality by one RF point to compensate for the lower resolution though.