What is the difference between Handbrake presets Apple TV2 vs Apple TV3?
Besides the resolution of course.
I noticed Apple TV3 takes longer even if the source file is not over 720p.
While the ATV2 preset is closer to the Normal preset (no decomb, fast adaptive B-frames and, of course, resizing), the ATV3 has a lot of additional settings making it slower (decomb, optimal adaptive B-frames etc.)
Nevertheless, you aren't forced to use the latter even for the ATV3. If you just use the Normal preset, it won't resize 1080p videos (unlike the ATV2 preset) and will produce great footage - quickly.