Surely the main consideration should be how the data is structured - ergo, if you do it in Flash it won't be, whereas if you do it in JS it can be.
The number of people who support Flash and the number who support JS are probably about the same (maybe slightly more flash) but at least with JS behaviors there's still something there underneath - the underlying data still has semantic form on the page. If you do it in Flash it's just embedded binary data - no structure or semantics there at all.
So I'd go with JS. There are still quite a few cool effects you can do - have a look at these -- http://www.brothercake.com/site/reso...s/transitions/