The formula is pretty simple. Bitrate x duration = file size.
So...larger file sizes mean either a higher bitrate, or a longer duration.
Yes, that makes sense. I think in my case the problem was caused by using the iPad 2 presets in CS6 as my starting point. The levels setting was set too high for the size of video I was exporting, therefore the higher file size. CS5.5 had more presets I think for the iPad 2 than just ones for 1080p video.
Things like resolution and frame rate won't make any difference. Only the bitrate and the duration.