You need to be much more specific...
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I have attempted my first Bluray rip with MakeMKV
which Mac and OS?
which bluray disc? was it a film or a TV show? what audio was on the disc and what did you include in the MakeMKV rip?
Have you tried to rip a different disc to compare results?
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I have encoded twice with Handbrake
which version of HB?
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once using the Apple 2 preset and the other modifying the settings to match what an article recommended
link to that article?
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Both times, the resulting movie exhibited choppy playback
Choppy playback on what? the Mac, an aTV2, an iPad, all of them? What are you using for playback, ideally, try it on the aTV2, and an iPad, and a Mac with various software players, like Plex and VLC.
Try to rule out your network or NAS causing the problem by moving the file around and try to rule out your display by playing it back on a machine connected to a different display. For instance, if you're using the aTV2 to play the file back, where "is" the file? Wired or wireless?
How does the original, full size MakeMKV rip play back with your Mac in Plex or XBMC?
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Is there a preset out there that offers good, consistent results? I also wasn't sure how I could get a 1080p out of Handbrake.
I think it's hard not to get good, consistent results with any of 3 or 4 presets...the Handbrake team has really, really stepped up their game. There are a few little tricks that can help with specific disc types, i.e. a few additional settings if the blu ray content was originally a TV show, but I think you should try out a few different discs and stay with the regular aTV2 preset for now. Approach this problem as if it has nothing to do with Handbrake per se, especially if you have only ripped one disc so far.
