Unless you use the same rendering settings results will vary a lot. Don't know what CS6 uses, or choices available, but you may have to take a small clip and render it in the various options to see what the size and quality are. At some point the size increases but the quality of playback appears the same.
When you render the video in CS6 see if you choose H.264 format instead of quicktime and preset pull-down menu High quality which will render a small mp4 file that Quicktime player should be able to play is OK for you. I do not know what CS6 does when you render video and choose quicktime the codec it uses generates that huge video file that does play???
unless im missing something here
cs5 has more options avalable for rendering mov then cs6, so in a way cs5 is more advanced
on the highest settings cs5 is able to render a smaller file size with the same quality render
I see that cs6 has mp4 available from media encoder, but i feel like its a step backwards since most of these videos still have to go though Media Encoder
... also Media Encoder doesn't have mov renders as an option
the reason why this is such a huge issue is that pptx files strictly take mov as a preferred video file, the whole adv industry runs on pptx presentations
cs5 - more options smaller files
cs6 - less options larger (unusable size) files